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NAR Web Server Issue 2009

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Databases

HMS-ICSTool Content

http://biodb.jp/

Computer Related > Databases

The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.

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tagsbiology database management systems genetic databases humans systems integration

Computer Related > Web Services

BioBIKETool Content

http://www.Biobike.org

Computer Related > Web Services

BioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.

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tagsbiology genetic databases systems integration

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

WebLabTool Content

http://weblab.cbi.pku.edu.cn

Computer Related > Web Services

An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.

This content is being maintained by Yang Ding.

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tagscomputational biology cooperative behavior factual databases

DNA > Annotations

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

GendooTool Content

http://gendoo.dbcls.jp

DNA > Annotations
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining and Semantics

Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

This content is being maintained by thecla.

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tagsdiabetes mellitus disease genes genetic databases medical subject headings

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene

DNA > Annotations
Literature > Text Mining and Semantics

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

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tagsanimals bone resorption controlled vocabulary gene expression profiling genes hepatoerythropoietic porphyria humans mice mutation oligonucleotide array sequence analysis osteoporosis pancreatic neoplasms pubmed rats

DNA > DNA and Genomic Analysis

OmicBrowseTool Content

http://sourceforge.net/projects/omicbrowse/

DNA > DNA and Genomic Analysis

OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.

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tagsgenetic databases genomics systems integration

DNA > Gene Prediction

HHompTool Content

http://toolkit.tuebingen.mpg.de/hhomp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.

This content is being maintained by mremmert.

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tagsamino acid sequence homology bacterial outer membrane proteins escherichia coli proteins protein databases

OrpheliaTool Content

http://orphelia.gobics.de

DNA > Gene Prediction

Orphelia is a machine learning program for predicting genes in short DNA sequences from metagenomic sequencing projects. The program encompasses fragment length specific prediction models for chain termination sequencing and pyrosequencing.

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tagsdna sequence analysis environmental microbiology genes genomics open reading frames

mGene.webTool Content

http://www.mgene.org/web

DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

DNA > Mapping and Assembly

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

TmPrimeTool Content

http://prime.ibn.a-star.edu.sg

DNA > Mapping and Assembly
DNA > Tools For the Bench

TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.

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tagsdna sequence analysis humans ligase chain reaction oligonucleotides polymerase chain reaction proteins synthetic genes

DNA > Phylogeny Reconstruction

OrthoSelectTool Content

http://orthoselect.gobics.de

DNA > Phylogeny Reconstruction
Expression > cDNA, EST, SAGE
Sequence Comparison > Pairwise Sequence Alignments

OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.

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tagsexpressed sequence tags genes genomics phylogeny sequence alignment

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

Virus Genotyping ToolsTool Content

http://bioafrica.mrc.ac.za/rega-genotype/html/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.

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tagsbase sequence genetic recombination genetic variation genotype hepacivirus hepatitis b virus hiv-1 phylogeny reference standards sequence alignment sequence analysis viruses

DNA > Sequence Polymorphisms

HomozygosityMapperTool Content

http://www.homozygositymapper.org

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.

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tagschromosome mapping genetic heterogeneity genetic linkage genotype homozygote reproducibility of results single nucleotide polymorphism

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

DNA > Sequence Retrieval and Submission

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

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tagsbiology genetic databases
setsOntario Institute for Cancer Research (OICR)

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

DNA > Structure and Sequence Feature Detection

3D-DARTTool Content

http://haddock.chem.uu.nl/dna/

DNA > Structure and Sequence Feature Detection

The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.

This content is being maintained by mvdijk.

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tagsdna molecular models nucleic acid conformation

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

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tagsbiology genetic databases
setsOntario Institute for Cancer Research (OICR)

HHompTool Content

http://toolkit.tuebingen.mpg.de/hhomp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.

This content is being maintained by mremmert.

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tagsamino acid sequence homology bacterial outer membrane proteins escherichia coli proteins protein databases

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

RegAnalystTool Content

http://www.nii.ac.in/~deepak/RegAnalyst/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes

RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).

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tagsbase sequence consensus sequence gene regulatory networks genetic promoter regions mycobacterium mycobacterium tuberculosis saccharomyces cerevisiae systems integration transcriptional regulatory elements

Web 3DNATool Content

http://w3dna.rutgers.edu

DNA > Structure and Sequence Feature Detection

The web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.

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tagscomputer-assisted image processing dna molecular models nucleic acid conformation rna

DNA > Tools For the Bench

GenoCADTool Content

http://www.genocad.org

DNA > Tools For the Bench
Expression > Networks
Expression > Protein Expression

GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.

This content is being maintained by peccoud.

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external linksLink on Twitter
tagsbase sequence chromosome mapping computer simulation dna gene database genetic code genetic engineering genetic models genomic islands nucleic acid databases reference standards synthetic genes

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

TmPrimeTool Content

http://prime.ibn.a-star.edu.sg

DNA > Mapping and Assembly
DNA > Tools For the Bench

TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.

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tagsdna sequence analysis humans ligase chain reaction oligonucleotides polymerase chain reaction proteins synthetic genes

UniPrime2Tool Content

http://uniprime.batlab.eu

DNA > Tools For the Bench

The UniPrime2 web server designs large sets of universal primers when provided with a gene reference ID or FASTA sequence. UniPrime2 works by integrating Blastn, T-Coffee, GramAlign and Primer3 into a single software pipeline.

This content is being maintained by mbekaert.

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tagsbase sequence conserved sequence dna primers dna sequence analysis nucleic acid sequence homology polymerase chain reaction

primers4cladesTool Content

http://maya.ccg.unam.mx/primers4clades/

DNA > Tools For the Bench
Protein > Phylogeny Reconstruction

Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.

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tagsalgorithms dna primers environmental microbiology genetic variation genomics phylogeny polymerase chain reaction reproducibility of results

Education > Directories and Portals

Bioinformatics Links DirectoryResource Content

http://www.bioinformatics.ca/links_directory/

Education > Directories and Portals

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

This content is being maintained by Francis Ouellette.

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tagscomputational biology directories as topic factual databases genetic databases genetics humans molecular biology
setsOntario Institute for Cancer Research (OICR)

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

Expression > Gene Regulation

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

GeneSet2miRNATool Content

http://mips.helmholtz-muenchen.de/proj/gene2mir/

Expression > Gene Regulation
Expression > Gene Set Analysis

GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.

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tagsanimals gene expression regulation genes humans mice micrornas rats

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MMIATool Content

http://cancer.informatics.indiana.edu/mmia

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Genomics
RNA > Functional RNAs

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

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tagsgenetic databases humans messenger rna micrornas rna interference

MirZTool Content

http://www.mirz.unibas.ch

Expression > Gene Regulation
Expression > cDNA, EST, SAGE
RNA > Functional RNAs

MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.

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tagsalgorithms animals genomics humans messenger rna mice micrornas rats rna interference systems integration

PscanTool Content

http://www.beaconlab.it/pscan

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

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tagsbinding sites dna sequence analysis gene expression regulation genetic promoter regions transcription factors

RegAnalystTool Content

http://www.nii.ac.in/~deepak/RegAnalyst/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes

RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).

NAR Web Server Issue 2009
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tagsbase sequence consensus sequence gene regulatory networks genetic promoter regions mycobacterium mycobacterium tuberculosis saccharomyces cerevisiae systems integration transcriptional regulatory elements

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

miRanalyzerTool Content

http://web.bioinformatics.cicbiogune.es/microRNA/

Expression > Gene Regulation
RNA > Functional RNAs

miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.

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tagsanimals dogs genetic transcription humans mice micrornas rats rna sequence analysis

Expression > Gene Set Analysis

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

G-SESAMETool Content

http://bioinformatics.clemson.edu/G-SESAME

Expression > Gene Set Analysis
Literature > Text Mining and Semantics
Sequence Comparison > Comparative Genomics

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

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tagscluster analysis controlled vocabulary genes genetic databases

GeSBAPTool Content

http://bioinfo.cipf.es/gesbap/

Expression > Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

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tagsbiological processes breast neoplasms female genes genetic variation genome-wide association study humans single nucleotide polymorphism

GendooTool Content

http://gendoo.dbcls.jp

DNA > Annotations
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining and Semantics

Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

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NAR Web Server Issue 2009
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tagsdiabetes mellitus disease genes genetic databases medical subject headings

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

GeneSet2miRNATool Content

http://mips.helmholtz-muenchen.de/proj/gene2mir/

Expression > Gene Regulation
Expression > Gene Set Analysis

GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.

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tagsanimals gene expression regulation genes humans mice micrornas rats

PscanTool Content

http://www.beaconlab.it/pscan

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

NAR Web Server Issue 2009
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tagsbinding sites dna sequence analysis gene expression regulation genetic promoter regions transcription factors

ToppGene SuiteTool Content

http://toppgene.cchmc.org

Expression > Gene Set Analysis
Expression > Networks

ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.

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tagsanimals disease genes humans mice protein interaction mapping proteins

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

VisHiCTool Content

http://biit.cs.ut.ee/vishic

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.

NAR Web Server Issue 2009
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tagsalgorithms cardiovascular diseases cluster analysis extracellular matrix gene expression profiling humans mitochondria myocardium oligonucleotide array sequence analysis

WhichGenesTool Content

http://www.whichgenes.org/

Expression > Gene Set Analysis

WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.

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tagsanimals genes genetic databases humans mice

Expression > Networks

GeneCodisTool Content

http://genecodis.dacya.ucm.es

Computer Related > Web Services
DNA > Annotations
Expression > Gene Set Analysis
Expression > Networks

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

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tagsanimals cattle gene expression regulation genes humans mice micrornas rats systems integration transcription factors

GenoCADTool Content

http://www.genocad.org

DNA > Tools For the Bench
Expression > Networks
Expression > Protein Expression

GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.

This content is being maintained by peccoud.

NAR Web Server Issue 2009
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tagsbase sequence chromosome mapping computer simulation dna gene database genetic code genetic engineering genetic models genomic islands nucleic acid databases reference standards synthetic genes

ToppGene SuiteTool Content

http://toppgene.cchmc.org

Expression > Gene Set Analysis
Expression > Networks

ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.

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tagsanimals disease genes humans mice protein interaction mapping proteins

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

Expression > Protein Expression

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

NAR Web Server Issue 2009
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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

GenoCADTool Content

http://www.genocad.org

DNA > Tools For the Bench
Expression > Networks
Expression > Protein Expression

GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.

This content is being maintained by peccoud.

NAR Web Server Issue 2009
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5
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external linksLink on Twitter
tagsbase sequence chromosome mapping computer simulation dna gene database genetic code genetic engineering genetic models genomic islands nucleic acid databases reference standards synthetic genes

Pomelo IITool Content

http://pomelo2.bioinfo.cnio.es

Expression > Protein Expression
Expression > Transcript Expression Analysis

Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.

This content is being maintained by rdiaz02.

NAR Web Server Issue 2009
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tagsgene expression profiling proteins reproducibility of results statistical data interpretation tissue array analysis

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

Expression > Splicing

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

SROOGLETool Content

http://sroogle.tau.ac.il

Expression > Splicing

SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.

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tagsexons introns ribonucleic acid regulatory sequences rna splice sites rna splicing systems integration

Expression > Transcript Expression Analysis

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

MMIATool Content

http://cancer.informatics.indiana.edu/mmia

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Genomics
RNA > Functional RNAs

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

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tagsgenetic databases humans messenger rna micrornas rna interference

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

Pomelo IITool Content

http://pomelo2.bioinfo.cnio.es

Expression > Protein Expression
Expression > Transcript Expression Analysis

Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.

This content is being maintained by rdiaz02.

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tagsgene expression profiling proteins reproducibility of results statistical data interpretation tissue array analysis

PscanTool Content

http://www.beaconlab.it/pscan

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

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tagsbinding sites dna sequence analysis gene expression regulation genetic promoter regions transcription factors

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

VisHiCTool Content

http://biit.cs.ut.ee/vishic

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.

NAR Web Server Issue 2009
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tagsalgorithms cardiovascular diseases cluster analysis extracellular matrix gene expression profiling humans mitochondria myocardium oligonucleotide array sequence analysis

Expression > cDNA, EST, SAGE

MirZTool Content

http://www.mirz.unibas.ch

Expression > Gene Regulation
Expression > cDNA, EST, SAGE
RNA > Functional RNAs

MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.

NAR Web Server Issue 2009
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tagsalgorithms animals genomics humans messenger rna mice micrornas rats rna interference systems integration

OrthoSelectTool Content

http://orthoselect.gobics.de

DNA > Phylogeny Reconstruction
Expression > cDNA, EST, SAGE
Sequence Comparison > Pairwise Sequence Alignments

OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.

NAR Web Server Issue 2009
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tagsexpressed sequence tags genes genomics phylogeny sequence alignment

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

WebGMAPTool Content

http://www.bioinfolab.org/software/webgmap

Expression > cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments

A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.

NAR Web Server Issue 2009
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tagschromosome mapping complementary dna dna sequence analysis genomics sequence alignment

Human Genome > Annotations

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

Human Genome > Genomics

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

GendooTool Content

http://gendoo.dbcls.jp

DNA > Annotations
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining and Semantics

Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

This content is being maintained by thecla.

NAR Web Server Issue 2009
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tagsdiabetes mellitus disease genes genetic databases medical subject headings

MMIATool Content

http://cancer.informatics.indiana.edu/mmia

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Genomics
RNA > Functional RNAs

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

NAR Web Server Issue 2009
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tagsgenetic databases humans messenger rna micrornas rna interference

WebGMAPTool Content

http://www.bioinfolab.org/software/webgmap

Expression > cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments

A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.

NAR Web Server Issue 2009
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tagschromosome mapping complementary dna dna sequence analysis genomics sequence alignment

mGene.webTool Content

http://www.mgene.org/web

DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

Human Genome > Health and Disease

GeSBAPTool Content

http://bioinfo.cipf.es/gesbap/

Expression > Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

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tagsbiological processes breast neoplasms female genes genetic variation genome-wide association study humans single nucleotide polymorphism

HomozygosityMapperTool Content

http://www.homozygositymapper.org

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.

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tagschromosome mapping genetic heterogeneity genetic linkage genotype homozygote reproducibility of results single nucleotide polymorphism

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

NAR Web Server Issue 2009
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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

OptiTopeTool Content

http://www.epitoolkit.org/optitope

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking

OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.

NAR Web Server Issue 2009
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tagsalleles epitopes humans major histocompatibility complex peptides subunit vaccines

PosMedTool Content

http://omicspace.riken.jp/PosMed/

Human Genome > Health and Disease
Literature > Text Mining and Semantics
Model Organisms > Mouse and Rat
Model Organisms > Plants

To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.

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tagsalgorithms animals arabidopsis genes humans medline mice molecular cloning neural networks (computer) rats

Human Genome > Sequence Polymorphisms

GeSBAPTool Content

http://bioinfo.cipf.es/gesbap/

Expression > Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

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tagsbiological processes breast neoplasms female genes genetic variation genome-wide association study humans single nucleotide polymorphism

HomozygosityMapperTool Content

http://www.homozygositymapper.org

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.

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tagschromosome mapping genetic heterogeneity genetic linkage genotype homozygote reproducibility of results single nucleotide polymorphism

OptiTopeTool Content

http://www.epitoolkit.org/optitope

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking

OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.

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tagsalleles epitopes humans major histocompatibility complex peptides subunit vaccines

Literature > Open Access Resources

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

Literature > Search Tools

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

Literature > Text Mining and Semantics

G-SESAMETool Content

http://bioinformatics.clemson.edu/G-SESAME

Expression > Gene Set Analysis
Literature > Text Mining and Semantics
Sequence Comparison > Comparative Genomics

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

NAR Web Server Issue 2009
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tagscluster analysis controlled vocabulary genes genetic databases

GendooTool Content

http://gendoo.dbcls.jp

DNA > Annotations
Expression > Gene Set Analysis
Human Genome > Genomics
Literature > Text Mining and Semantics

Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

This content is being maintained by thecla.

NAR Web Server Issue 2009
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tagsdiabetes mellitus disease genes genetic databases medical subject headings

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene

DNA > Annotations
Literature > Text Mining and Semantics

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

NAR Web Server Issue 2009
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tagsanimals bone resorption controlled vocabulary gene expression profiling genes hepatoerythropoietic porphyria humans mice mutation oligonucleotide array sequence analysis osteoporosis pancreatic neoplasms pubmed rats

LitInspectorTool Content

http://www.litinspector.org/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.

NAR Web Server Issue 2009
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tagsanimals humans mice pubmed rats signal transduction terminology as topic

MedlineRankerTool Content

http://cbdm.mdc-berlin.de/tools/medlineranker

Literature > Text Mining and Semantics

The MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge.

This content is being maintained by fontaine.

NAR Web Server Issue 2009
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tagsbayesian classifier document retrieval medline text mining

PLAN2LTool Content

http://zope.bioinfo.cnio.es/plan2l

Literature > Text Mining and Semantics
Model Organisms > Plants

A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.

NAR Web Server Issue 2009
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tagsarabidopsis arabidopsis agamous protein arabidopsis proteins systems integration transcription factors

PosMedTool Content

http://omicspace.riken.jp/PosMed/

Human Genome > Health and Disease
Literature > Text Mining and Semantics
Model Organisms > Mouse and Rat
Model Organisms > Plants

To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.

NAR Web Server Issue 2009
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tagsalgorithms animals arabidopsis genes humans medline mice molecular cloning neural networks (computer) rats

SENTTool Content

http://sent.dacya.ucm.es

Literature > Text Mining and Semantics

SENT is a text mining web server. SENT uses non-negative matrix factorization to identify topics in scientific articles associated with an input list of genes.

NAR Web Server Issue 2009
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tagsgenes humans

Model Organisms > Fly

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

Model Organisms > General Resources

mGene.webTool Content

http://www.mgene.org/web

DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

Model Organisms > Microbes

ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

CVTreeTool Content

http://tlife.fudan.edu.cn/cvtree

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

HHompTool Content

http://toolkit.tuebingen.mpg.de/hhomp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.

This content is being maintained by mremmert.

NAR Web Server Issue 2009
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tagsamino acid sequence homology bacterial outer membrane proteins escherichia coli proteins protein databases

InsigniaTool Content

http://insignia.cbcb.umd.edu

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.

NAR Web Server Issue 2009
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tagsanimals bacteria bacterial genome dna sequence analysis humans infection viral genome viruses

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

NAR Web Server Issue 2009
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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

Microbe BrowserTool Content

http://microbe.vital-it.ch

Model Organisms > Microbes

The Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.

NAR Web Server Issue 2009
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tagsarchaeal genome bacterial chromosomes bacterial genome genomics

RegAnalystTool Content

http://www.nii.ac.in/~deepak/RegAnalyst/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes

RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).

NAR Web Server Issue 2009
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tagsbase sequence consensus sequence gene regulatory networks genetic promoter regions mycobacterium mycobacterium tuberculosis saccharomyces cerevisiae systems integration transcriptional regulatory elements

Virus Genotyping ToolsTool Content

http://bioafrica.mrc.ac.za/rega-genotype/html/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.

NAR Web Server Issue 2009
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tagsbase sequence genetic recombination genetic variation genotype hepacivirus hepatitis b virus hiv-1 phylogeny reference standards sequence alignment sequence analysis viruses

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

Model Organisms > Mouse and Rat

PosMedTool Content

http://omicspace.riken.jp/PosMed/

Human Genome > Health and Disease
Literature > Text Mining and Semantics
Model Organisms > Mouse and Rat
Model Organisms > Plants

To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.

NAR Web Server Issue 2009
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tagsalgorithms animals arabidopsis genes humans medline mice molecular cloning neural networks (computer) rats

Model Organisms > Other Organisms

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

Model Organisms > Plants

PLAN2LTool Content

http://zope.bioinfo.cnio.es/plan2l

Literature > Text Mining and Semantics
Model Organisms > Plants

A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.

NAR Web Server Issue 2009
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tagsarabidopsis arabidopsis agamous protein arabidopsis proteins systems integration transcription factors

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

PREP SuiteTool Content

http://prep.unl.edu/

Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

PosMedTool Content

http://omicspace.riken.jp/PosMed/

Human Genome > Health and Disease
Literature > Text Mining and Semantics
Model Organisms > Mouse and Rat
Model Organisms > Plants

To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.

NAR Web Server Issue 2009
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tagsalgorithms animals arabidopsis genes humans medline mice molecular cloning neural networks (computer) rats

Model Organisms > Worm

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

Other Molecules > Compounds

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

This content is being maintained by flebeda.

NAR Web Server Issue 2009
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SePreSATool Content

http://SePreSA.Bio-X.cn/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.

NAR Web Server Issue 2009
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tagsalgorithms binding sites drug toxicity genetic polymorphism humans molecular models pharmaceutical preparations protein conformation proteins

wwLigCSRreTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/wwLigCSRre.html

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison

The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.

NAR Web Server Issue 2009
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tagscyclin-dependent kinase 2 drug design factual databases igf type 1 receptor ligands molecular models protein kinase inhibitors small molecule libraries structure-activity relationship

Other Molecules > Metabolites

FMMTool Content

http://FMM.mbc.nctu.edu.tw/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

MetaboAnalystTool Content

http://www.metaboanalyst.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis.

This content is being maintained by Jeff Xia.

NAR Web Server Issue 2009
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tagsbiomolecular nuclear magnetic resonance cluster analysis mass spectrometry metabolomics

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

Other Molecules > Small Molecules

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

This content is being maintained by flebeda.

NAR Web Server Issue 2009
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

wwLigCSRreTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/wwLigCSRre.html

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison

The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.

NAR Web Server Issue 2009
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tagscyclin-dependent kinase 2 drug design factual databases igf type 1 receptor ligands molecular models protein kinase inhibitors small molecule libraries structure-activity relationship

Protein > 2-D Structure Prediction

NetCSSPTool Content

http://cssp2.sookmyung.ac.kr

Protein > 2-D Structure Prediction

A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.

NAR Web Server Issue 2009
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tagsalgorithms amyloid protein sequence analysis secondary protein structure

ProSMoSTool Content

http://prodata.swmed.edu/ProSMoS/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.

NAR Web Server Issue 2009
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tagsmolecular models protein databases secondary protein structure

TOPCONSTool Content

http://topcons.net

Protein > 2-D Structure Prediction
Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.

NAR Web Server Issue 2009
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tagsalgorithms membrane proteins protein conformation reproducibility of results

Protein > 3-D Structural Features

MolLocTool Content

http://bcb.dei.unipd.it/MolLoc

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Molecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.

NAR Web Server Issue 2009
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tagsbinding sites dna molecular models nucleic acid conformation protein structural homology proteins rna

NNconTool Content

http://casp.rnet.missouri.edu/nncon.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.

NAR Web Server Issue 2009
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tagsmolecular models neural networks (computer) protein conformation protein folding reproducibility of results

PHEMTOTool Content

http://phemto.orgchm.bas.bg/

Protein > 3-D Structural Features
Protein > Biochemical Features

Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.

NAR Web Server Issue 2009
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tagsalgorithms hydrogen-ion concentration proteins static electricity

ProSMoSTool Content

http://prodata.swmed.edu/ProSMoS/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.

NAR Web Server Issue 2009
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tagsmolecular models protein databases secondary protein structure

RASMOT-3D PROTool Content

http://biodev.extra.cea.fr/rasmot3d/

Protein > 3-D Structural Features

The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.

NAR Web Server Issue 2009
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tagsamino acid motifs ligands molecular models protein databases

RHYTHMTool Content

http://proteinformatics.charite.de/rhythm/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.

NAR Web Server Issue 2009
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tagsmembrane proteins membrane transport proteins molecular models reproducibility of results secondary protein structure tertiary protein structure

SITEHOUND-webTool Content

http://sitehound.sanchezlab.org

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.

NAR Web Server Issue 2009
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tagsalgorithms binding sites ligands protein conformation

SLITHERTool Content

http://bioinfo.mc.ntu.edu.tw/slither/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.

NAR Web Server Issue 2009
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tagscatalytic domain glucose transporter type 1 humans ligands membrane transport proteins molecular models protein conformation

SplitPocketTool Content

http://pocket.uchicago.edu/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.

NAR Web Server Issue 2009
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tagscatalytic domain humans ligands mitogen-activated protein kinases molecular models protein conformation proteins src-family kinases

SuperLooperTool Content

http://bioinf-applied.charite.de/superlooper/

Protein > 3-D Structural Features

SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.

NAR Web Server Issue 2009
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tagsmembrane proteins molecular models protein conformation protein databases reproducibility of results

seeMotifTool Content

http://seemotif.csie.ntu.edu.tw

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).

This content is being maintained by dirty.

NAR Web Server Issue 2009
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tagsamino acid motifs molecular models protein databases

Protein > 3-D Structure Comparison

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

COPSTool Content

http://cops.services.came.sbg.ac.at/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

HorATool Content

http://prodata.swmed.edu/horaserver/

Protein > 3-D Structure Comparison
Sequence Comparison > Similarity Searching

HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.

NAR Web Server Issue 2009
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tagsamino acid sequence homology ef hand motifs molecular models protein structural homology reproducibility of results

MolLocTool Content

http://bcb.dei.unipd.it/MolLoc

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Molecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.

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tagsbinding sites dna molecular models nucleic acid conformation protein structural homology proteins rna

ProSMoSTool Content

http://prodata.swmed.edu/ProSMoS/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.

NAR Web Server Issue 2009
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tagsmolecular models protein databases secondary protein structure

SALAMITool Content

http://www.zbh.uni-hamburg.de/salami

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments.

NAR Web Server Issue 2009
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tagsamino acid sequence protein databases protein structural homology sequence alignment

SARATool Content

http://sgu.bioinfo.cipf.es/services/SARA/

Protein > 3-D Structure Comparison
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment.

This content is being maintained by marcius.

NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna rna function prediction rna structure alignment

iSARSTTool Content

http://sarst.life.nthu.edu.tw/iSARST/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Proteomics

iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.

NAR Web Server Issue 2009
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tagsprotein databases protein structural homology systems integration

wwLigCSRreTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/wwLigCSRre.html

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison

The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.

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tagscyclin-dependent kinase 2 drug design factual databases igf type 1 receptor ligands molecular models protein kinase inhibitors small molecule libraries structure-activity relationship

Protein > 3-D Structure Prediction

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

GeNMRTool Content

http://www.genmr.ca

Protein > 3-D Structure Prediction

Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.

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tagsalgorithms biomolecular nuclear magnetic resonance molecular models protein conformation protein databases reproducibility of results

NNconTool Content

http://casp.rnet.missouri.edu/nncon.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.

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tagsmolecular models neural networks (computer) protein conformation protein folding reproducibility of results

PEP-FOLDTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD

Protein > 3-D Structure Prediction

PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution.

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tagsalgorithms molecular models peptides protein conformation protein sequence analysis reproducibility of results

QMEANTool Content

http://swissmodel.expasy.org/qmean

Protein > 3-D Structure Prediction

QMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used.

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tagsblood coagulation humans lipopolysaccharides monocytes thiopental thromboplastin

RHYTHMTool Content

http://proteinformatics.charite.de/rhythm/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.

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tagsmembrane proteins membrane transport proteins molecular models reproducibility of results secondary protein structure tertiary protein structure

RosettaAntibodyTool Content

http://antibody.graylab.jhu.edu

Protein > 3-D Structure Prediction

The RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being returned in high resolution and detailed format.

This content is being maintained by aroopsircar.

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tagsalgorithms amino acid sequence homology antibody modeling antibody modeling server CDR detection chothia numbering complementarity determining regions immunoglobulin heavy chains immunoglobulin light chains immunoglobulin variable region molecular models webserver

SEPPATool Content

http://lifecenter.sgst.cn/seppa/index.php

Protein > 3-D Structure Prediction

A computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.

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tagscomputational biology epitope mapping epitopes proteins reproducibility of results

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

Protein > 3-D Structure Retrieval/Viewing

COPSTool Content

http://cops.services.came.sbg.ac.at/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

SALAMITool Content

http://www.zbh.uni-hamburg.de/salami

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments.

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tagsamino acid sequence protein databases protein structural homology sequence alignment

iSARSTTool Content

http://sarst.life.nthu.edu.tw/iSARST/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Proteomics

iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.

NAR Web Server Issue 2009
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tagsprotein databases protein structural homology systems integration

seeMotifTool Content

http://seemotif.csie.ntu.edu.tw

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).

This content is being maintained by dirty.

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tagsamino acid motifs molecular models protein databases

Protein > Annotation and Function

ANNIETool Content

http://annie.bii.a-star.edu.sg

Protein > Annotation and Function

ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.

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tagsalgorithms protein sequence analysis

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

INTREPIDTool Content

http://phylogenomics.berkeley.edu/intrepid

Protein > Annotation and Function
Protein > Sequence Features

The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.

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tagsamino acid sequence homology amino acids catalytic domain molecular models phylogeny protein conformation protein sequence analysis proteins

ProGMapTool Content

http://www.bioinformatics.nl/progmap

Protein > Annotation and Function
Protein > Proteomics
Protein > Sequence Comparison

Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.

NAR Web Server Issue 2009
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tagsprotein databases protein sequence analysis proteins systems integration

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

Protein > Biochemical Features

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

This content is being maintained by flebeda.

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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

PHEMTOTool Content

http://phemto.orgchm.bas.bg/

Protein > 3-D Structural Features
Protein > Biochemical Features

Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.

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tagsalgorithms hydrogen-ion concentration proteins static electricity

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SLITHERTool Content

http://bioinfo.mc.ntu.edu.tw/slither/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.

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tagscatalytic domain glucose transporter type 1 humans ligands membrane transport proteins molecular models protein conformation

Protein > Do-it-all Tools for Protein

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

Protein > Domains and Motifs

COPSTool Content

http://cops.services.came.sbg.ac.at/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

ProteDNATool Content

http://protedna.csbb.ntu.edu.tw/

Protein > Domains and Motifs
Protein > Sequence Features

ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.

NAR Web Server Issue 2009
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tagsbase sequence binding sites dna dna-binding proteins protein sequence analysis transcription factors

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

seeMotifTool Content

http://seemotif.csie.ntu.edu.tw

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).

This content is being maintained by dirty.

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tagsamino acid motifs molecular models protein databases

webPRCTool Content

http://www.ibi.vu.nl/programs/prcwww/

Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments

Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.

NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology markov chains protein databases sequence alignment tertiary protein structure

Protein > Interactions, Pathways, Enzymes

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

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tagsbiology genetic databases
setsOntario Institute for Cancer Research (OICR)

DASMIwebDatabase Content

http://www.dasmiweb.de

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.

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tagsonline systems protein interaction domains and motifs protein interaction mapping systems integration

FMMTool Content

http://FMM.mbc.nctu.edu.tw/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

LitInspectorTool Content

http://www.litinspector.org/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.

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tagsanimals humans mice pubmed rats signal transduction terminology as topic

MetaboAnalystTool Content

http://www.metaboanalyst.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis.

This content is being maintained by Jeff Xia.

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tagsbiomolecular nuclear magnetic resonance cluster analysis mass spectrometry metabolomics

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

Protinfo PPCTool Content

http://protinfo.compbio.washington.edu/ppc/

Protein > Interactions, Pathways, Enzymes

Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.

This content is being maintained by weerayuth.

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tagsmolecular models multiprotein complexes protein conformation protein databases protein sequence analysis reproducibility of results

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SITEHOUND-webTool Content

http://sitehound.sanchezlab.org

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.

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tagsalgorithms binding sites ligands protein conformation

SNOWTool Content

http://snow.bioinfo.cipf.es

Protein > Interactions, Pathways, Enzymes

SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates.

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tagshumans protein databases protein interaction mapping statistical data interpretation

SePreSATool Content

http://SePreSA.Bio-X.cn/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.

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tagsalgorithms binding sites drug toxicity genetic polymorphism humans molecular models pharmaceutical preparations protein conformation proteins

TorqueTool Content

http://www.cs.tau.ac.il/~bnet/torque.html

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction

Torque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.

NAR Web Server Issue 2009
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tagsprotein interaction mapping protein sequence analysis

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

Protein > Localization and Targeting

RHYTHMTool Content

http://proteinformatics.charite.de/rhythm/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.

NAR Web Server Issue 2009
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tagsmembrane proteins membrane transport proteins molecular models reproducibility of results secondary protein structure tertiary protein structure

Protein > Molecular Dynamics and Docking

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

OptiTopeTool Content

http://www.epitoolkit.org/optitope

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking

OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolKit.

NAR Web Server Issue 2009
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tagsalleles epitopes humans major histocompatibility complex peptides subunit vaccines

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SITEHOUND-webTool Content

http://sitehound.sanchezlab.org

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation.

NAR Web Server Issue 2009
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tagsalgorithms binding sites ligands protein conformation

SLITHERTool Content

http://bioinfo.mc.ntu.edu.tw/slither/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.

NAR Web Server Issue 2009
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tagscatalytic domain glucose transporter type 1 humans ligands membrane transport proteins molecular models protein conformation

SePreSATool Content

http://SePreSA.Bio-X.cn/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.

NAR Web Server Issue 2009
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tagsalgorithms binding sites drug toxicity genetic polymorphism humans molecular models pharmaceutical preparations protein conformation proteins

SplitPocketTool Content

http://pocket.uchicago.edu/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.

NAR Web Server Issue 2009
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tagscatalytic domain humans ligands mitogen-activated protein kinases molecular models protein conformation proteins src-family kinases

Protein > Phylogeny Reconstruction

CVTreeTool Content

http://tlife.fudan.edu.cn/cvtree

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

PHOGTool Content

http://phylofacts.berkeley.edu/orthologs/

Protein > Phylogeny Reconstruction

The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.

NAR Web Server Issue 2009
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tagsalgorithms animals humans mice phylogeny protein sequence analysis reproducibility of results

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

NAR Web Server Issue 2009
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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping

PhyloParsTool Content

http://www.ibi.vu.nl/programs/phylopars/

Protein > Phylogeny Reconstruction

The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.

NAR Web Server Issue 2009
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tagsphenotype phylogeny phytoplankton

TorqueTool Content

http://www.cs.tau.ac.il/~bnet/torque.html

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction

Torque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.

NAR Web Server Issue 2009
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tagsprotein interaction mapping protein sequence analysis

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

primers4cladesTool Content

http://maya.ccg.unam.mx/primers4clades/

DNA > Tools For the Bench
Protein > Phylogeny Reconstruction

Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.

NAR Web Server Issue 2009
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tagsalgorithms dna primers environmental microbiology genetic variation genomics phylogeny polymerase chain reaction reproducibility of results

Protein > Protein Expression

AutoClass@IJMTool Content

http://www.ijm.fr/en/ijm/resources/bioinformatics/

Expression > Gene Set Analysis
Expression > Protein Expression
Expression > Transcript Expression Analysis
Human Genome > Genomics
Protein > Protein Expression

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

NAR Web Server Issue 2009
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tagsalgorithms bayes theorem classification cluster analysis gene expression profiling oligonucleotide array sequence analysis

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

Protein > Proteomics

MaXIC-QTool Content

http://ms.iis.sinica.edu.tw/MaXIC-Q

Protein > Proteomics

The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.

NAR Web Server Issue 2009
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tagscomputational biology endothelial cells isotope labeling liquid chromatography mass spectrometry nitric acid peptides proteins reproducibility of results statistical data interpretation

MetaboAnalystTool Content

http://www.metaboanalyst.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis.

This content is being maintained by Jeff Xia.

NAR Web Server Issue 2009
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tagsbiomolecular nuclear magnetic resonance cluster analysis mass spectrometry metabolomics

ProGMapTool Content

http://www.bioinformatics.nl/progmap

Protein > Annotation and Function
Protein > Proteomics
Protein > Sequence Comparison

Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.

NAR Web Server Issue 2009
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tagsprotein databases protein sequence analysis proteins systems integration

iSARSTTool Content

http://sarst.life.nthu.edu.tw/iSARST/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Proteomics

iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.

NAR Web Server Issue 2009
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tagsprotein databases protein structural homology systems integration

Protein > Sequence Comparison

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

NAR Web Server Issue 2009
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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping

ProGMapTool Content

http://www.bioinformatics.nl/progmap

Protein > Annotation and Function
Protein > Proteomics
Protein > Sequence Comparison

Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.

NAR Web Server Issue 2009
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tagsprotein databases protein sequence analysis proteins systems integration

TOPCONSTool Content

http://topcons.net

Protein > 2-D Structure Prediction
Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.

NAR Web Server Issue 2009
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tagsalgorithms membrane proteins protein conformation reproducibility of results

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

Protein > Sequence Data

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

Protein > Sequence Features

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

INTREPIDTool Content

http://phylogenomics.berkeley.edu/intrepid

Protein > Annotation and Function
Protein > Sequence Features

The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.

NAR Web Server Issue 2009
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tagsamino acid sequence homology amino acids catalytic domain molecular models phylogeny protein conformation protein sequence analysis proteins

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

ProteDNATool Content

http://protedna.csbb.ntu.edu.tw/

Protein > Domains and Motifs
Protein > Sequence Features

ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.

NAR Web Server Issue 2009
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tagsbase sequence binding sites dna dna-binding proteins protein sequence analysis transcription factors

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

Protein > Sequence Retrieval

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

NAR Web Server Issue 2009
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tagsbiology genetic databases
setsOntario Institute for Cancer Research (OICR)

DASMIwebDatabase Content

http://www.dasmiweb.de

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.

NAR Web Server Issue 2009
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tagsonline systems protein interaction domains and motifs protein interaction mapping systems integration

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

RNA > Databases

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

NAR Web Server Issue 2009
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tagsbiology genetic databases
setsOntario Institute for Cancer Research (OICR)

RNA > Functional RNAs

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

MMIATool Content

http://cancer.informatics.indiana.edu/mmia

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Genomics
RNA > Functional RNAs

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

NAR Web Server Issue 2009
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tagsgenetic databases humans messenger rna micrornas rna interference

MirZTool Content

http://www.mirz.unibas.ch

Expression > Gene Regulation
Expression > cDNA, EST, SAGE
RNA > Functional RNAs

MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.

NAR Web Server Issue 2009
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tagsalgorithms animals genomics humans messenger rna mice micrornas rats rna interference systems integration

SARATool Content

http://sgu.bioinfo.cipf.es/services/SARA/

Protein > 3-D Structure Comparison
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment.

This content is being maintained by marcius.

NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna rna function prediction rna structure alignment

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo

DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

miRanalyzerTool Content

http://web.bioinformatics.cicbiogune.es/microRNA/

Expression > Gene Regulation
RNA > Functional RNAs

miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.

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tagsanimals dogs genetic transcription humans mice micrornas rats rna sequence analysis

RNA > Motifs

PREP SuiteTool Content

http://prep.unl.edu/

Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

RNA > Sequence Retrieval

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

RNA > Structure Prediction, Visualization, and Design

CentroidFoldTool Content

http://www.ncrna.org/centroidfold/

RNA > Structure Prediction, Visualization, and Design

Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).

NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna sequence analysis sequence alignment transfer rna untranslated rna

RNAmutantsTool Content

http://bioinformatics.bc.edu/clotelab/RNAmutants/

RNA > Structure Prediction, Visualization, and Design

A web server to explore the effect of mutations on the RNA secondary structures.

NAR Web Server Issue 2009
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tagsnucleic acid conformation point mutation rna sequence analysis untranslated rna

SARATool Content

http://sgu.bioinfo.cipf.es/services/SARA/

Protein > 3-D Structure Comparison
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment.

This content is being maintained by marcius.

NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna rna function prediction rna structure alignment

Sequence Comparison > Alignment Editing and Visualization

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

WebGMAPTool Content

http://www.bioinfolab.org/software/webgmap

Expression > cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments

A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.

NAR Web Server Issue 2009
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tagschromosome mapping complementary dna dna sequence analysis genomics sequence alignment

Sequence Comparison > Analysis of Aligned Sequences

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

ClanToxTool Content

http://www.clantox.cs.huji.ac.il

Sequence Comparison > Analysis of Aligned Sequences

ClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.

NAR Web Server Issue 2009
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tagsanimals biological toxins cysteine protein sequence analysis proteomics

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

Sequence Comparison > Comparative Genomics

ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

G-SESAMETool Content

http://bioinformatics.clemson.edu/G-SESAME

Expression > Gene Set Analysis
Literature > Text Mining and Semantics
Sequence Comparison > Comparative Genomics

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

NAR Web Server Issue 2009
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tagscluster analysis controlled vocabulary genes genetic databases

InsigniaTool Content

http://insignia.cbcb.umd.edu

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.

NAR Web Server Issue 2009
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tagsanimals bacteria bacterial genome dna sequence analysis humans infection viral genome viruses

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

NAR Web Server Issue 2009
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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

Sequence Comparison > Multiple Sequence Alignments

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

webPRCTool Content

http://www.ibi.vu.nl/programs/prcwww/

Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments

Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.

NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology markov chains protein databases sequence alignment tertiary protein structure

Sequence Comparison > Pairwise Sequence Alignments

MGIPTool Content

http://mgip.biology.gatech.edu

DNA > Mapping and Assembly
Human Genome > Health and Disease
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics
Sequence Comparison > Pairwise Sequence Alignments

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

NAR Web Server Issue 2009
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tagsalleles bacterial genome bacterial typing techniques dna sequence analysis genomics neisseria meningitidis reproducibility of results

OrthoSelectTool Content

http://orthoselect.gobics.de

DNA > Phylogeny Reconstruction
Expression > cDNA, EST, SAGE
Sequence Comparison > Pairwise Sequence Alignments

OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.

NAR Web Server Issue 2009
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tagsexpressed sequence tags genes genomics phylogeny sequence alignment

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

SIB-BLASTTool Content

http://sib-blast.osc.edu

Sequence Comparison > Pairwise Sequence Alignments

SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.

This content is being maintained by rbund.

NAR Web Server Issue 2009
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tagsalgorithms amino acid sequence homology sequence alignment

TOPCONSTool Content

http://topcons.net

Protein > 2-D Structure Prediction
Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.

NAR Web Server Issue 2009
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tagsalgorithms membrane proteins protein conformation reproducibility of results

WebGMAPTool Content

http://www.bioinfolab.org/software/webgmap

Expression > cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments

A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.

NAR Web Server Issue 2009
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tagschromosome mapping complementary dna dna sequence analysis genomics sequence alignment

Sequence Comparison > Similarity Searching

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

HorATool Content

http://prodata.swmed.edu/horaserver/

Protein > 3-D Structure Comparison
Sequence Comparison > Similarity Searching

HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.

NAR Web Server Issue 2009
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tagsamino acid sequence homology ef hand motifs molecular models protein structural homology reproducibility of results

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping