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NAR Web Server Issue 2008

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DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

DNA > Annotations

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

Ontology Lookup ServiceTool Content

http://www.ebi.ac.uk/ols

DNA > Annotations
DNA > DNA and Genomic Analysis
Model Organisms > General Resources

The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.

This content is being maintained by rglcote.

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tagscontrolled vocabulary database management systems factual databases natural language processing programming languages proteomics systems integration

DNA > DNA and Genomic Analysis

Ontology Lookup ServiceTool Content

http://www.ebi.ac.uk/ols

DNA > Annotations
DNA > DNA and Genomic Analysis
Model Organisms > General Resources

The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.

This content is being maintained by rglcote.

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tagscontrolled vocabulary database management systems factual databases natural language processing programming languages proteomics systems integration

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

xREITool Content

http://biowiki.org/XreiProgram

DNA > DNA and Genomic Analysis
DNA > Gene Prediction
Protein > 2-D Structure Prediction
RNA > Functional RNAs

xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.

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tagsdna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment statistical models

DNA > Gene Prediction

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

xREITool Content

http://biowiki.org/XreiProgram

DNA > DNA and Genomic Analysis
DNA > Gene Prediction
Protein > 2-D Structure Prediction
RNA > Functional RNAs

xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.

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tagsdna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment statistical models

DNA > Phylogeny Reconstruction

CRISPRcomparTool Content

http://crispr.u-psud.fr/CRISPRcompar/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.

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tagsalleles bacteria bacterial typing techniques tandem repeat sequences

SignatureTool Content

http://www.cmbi.ru.nl/signature

DNA > Phylogeny Reconstruction

Signature identifies signature genes or genes that are unique to a taxonomic clade and thus useful in phylogenetic analysis. Users input a set of query sequences and returned is a list of taxonomic clades that share signatures with the query.

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tagsbiological evolution genes phylogeny protein sequence analysis sequence alignment

DNA > Sequence Polymorphisms

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.

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tagsalgorithms cluster analysis drug dose-response relationship gene expression profiling genetic polymorphism kinetics oligonucleotide array sequence analysis systems integration

MKTTool Content

http://mkt.uab.es

DNA > Sequence Polymorphisms

Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.

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tagsanimals codon dna sequence analysis drosophila genetic selection genetic variation

QUMATool Content

http://quma.cdb.riken.jp/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

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tagscpg islands dna methylation dna sequence analysis statistical data interpretation sulfites

DNA > Sequence Retrieval and Submission

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

DNA > Structure and Sequence Feature Detection

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

ConTraTool Content

http://bioit.dmbr.ugent.be/ConTra/index.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

The Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcription factor binding sites predicted using TransFac, JASPAR or PWM libraries on aligned promoter sequences. Nine reference organisms are supported for analysis of promoter regions, 5' UTRs, 3' UTRs and introns.

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tagsanimals binding sites dna sequence analysis genetic promoter regions humans sequence alignment transcription factors

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

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tagsalgorithms cluster analysis computational biology gene expression profiling

DNA > Tools For the Bench

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeRTool Content

http://guinevere.otago.ac.nz/stats.html

DNA > Tools For the Bench

GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.

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tagsalgorithms chemical models codon computer simulation directed molecular evolution dna dna mutational analysis dna sequence analysis gene library genetic models genetic variation molecular evolution mutagenesis mutation peptide library point mutation polymerase chain reaction protein sequence analysis proteins statistical models

IDT SciToolsTool Content

http://www.idtdna.com/SciTools/SciTools.aspx

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.

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tagsantisense oligonucleotides dna primers nucleic acid conformation oligonucleotide probes oligonucleotides small interfering rna

OligoHeatMapTool Content

http://bioinfo.unice.fr/ohm/

DNA > Tools For the Bench

OligoHeatMap is an online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically.

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tagsdna sequence analysis nucleic acid denaturation nucleic acid hybridization oligonucleotide probes polymerase chain reaction sequence alignment thermodynamics

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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external linksLink on TwitterLink on Wikipedia
tagscomputational biology directories as topic factual databases genetic databases genetics humans molecular biology
setsOntario Institute for Cancer Research (OICR)

Expression > Gene Regulation

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

ConTraTool Content

http://bioit.dmbr.ugent.be/ConTra/index.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

The Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcription factor binding sites predicted using TransFac, JASPAR or PWM libraries on aligned promoter sequences. Nine reference organisms are supported for analysis of promoter regions, 5' UTRs, 3' UTRs and introns.

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tagsanimals binding sites dna sequence analysis genetic promoter regions humans sequence alignment transcription factors

DiRETool Content

http://dire.dcode.org

Expression > Gene Regulation

A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.

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tagsanimals binding sites gene expression profiling gene expression regulation genetic enhancer elements genetic promoter regions genomics humans transcription factors transcriptional regulatory elements

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

Expression > Networks

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

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tagscluster analysis factual databases metabolic networks and pathways

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

GraphWebTool Content

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

Expression > Networks

GraphWeb is a web server for biological network analysis and module design using a graphical interface.

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tagscell cycle proteins gene expression profiling gene regulatory networks humans protein interaction mapping

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MADNetTool Content

http://www.bioinfo.hr/madnet

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

NeATTool Content

http://rsat.ulb.ac.be/neat/

Expression > Networks

Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.

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tagscluster analysis gene expression regulation metabolic networks and pathways oligonucleotide array sequence analysis protein interaction mapping signal transduction

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

Expression > Protein Expression

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

GOEASTTool Content

http://omicslab.genetics.ac.cn/GOEAST/

Expression > Protein Expression
Expression > Transcript Expression Analysis

Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.

This content is being maintained by e00011027.

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tagscontrolled vocabulary gene expression profiling genes oligonucleotide array sequence analysis

MADNetTool Content

http://www.bioinfo.hr/madnet

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

ProfComTool Content

http://webclu.bio.wzw.tum.de/profcom/

Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.

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tagsanimals gene expression profiling genes humans mice rabbits

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

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tagsalgorithms cluster analysis computational biology gene expression profiling

Expression > Transcript Expression Analysis

AMIC@Tool Content

http://bioalgo.iit.cnr.it/amica

Expression > Transcript Expression Analysis

The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.

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tagsalgorithms cluster analysis gene expression profiling oligonucleotide array sequence analysis

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

CoPubTool Content

http://www.copub.org

Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

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tagsanimals gene expression profiling humans medline mice oligonucleotide array sequence analysis rats

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.

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tagsalgorithms cluster analysis drug dose-response relationship gene expression profiling genetic polymorphism kinetics oligonucleotide array sequence analysis systems integration

GOEASTTool Content

http://omicslab.genetics.ac.cn/GOEAST/

Expression > Protein Expression
Expression > Transcript Expression Analysis

Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.

This content is being maintained by e00011027.

NAR Web Server Issue 2008
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tagscontrolled vocabulary gene expression profiling genes oligonucleotide array sequence analysis

GeneCATTool Content

http://genecat.mpg.de

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Plants

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

NAR Web Server Issue 2008
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tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

MADNetTool Content

http://www.bioinfo.hr/madnet

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

Microarray RetrieverTool Content

http://www.lgtc.nl/MaRe/

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.

NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases meta-analysis as topic oligonucleotide array sequence analysis

PaLSTool Content

http://pals.bioinfo.cnio.es

Expression > Transcript Expression Analysis
Protein > Proteomics

Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.

This content is being maintained by aalibes.

NAR Web Server Issue 2008
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tagscontrolled vocabulary factual databases gene expression profiling genes metabolic networks and pathways proteins pubmed

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

ProfComTool Content

http://webclu.bio.wzw.tum.de/profcom/

Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.

NAR Web Server Issue 2008
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tagsanimals gene expression profiling genes humans mice rabbits

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

Expression > cDNA, EST, SAGE

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

NAR Web Server Issue 2008
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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

GeneCATTool Content

http://genecat.mpg.de

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Plants

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

NAR Web Server Issue 2008
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tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

MADNetTool Content

http://www.bioinfo.hr/madnet

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

Microarray RetrieverTool Content

http://www.lgtc.nl/MaRe/

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.

NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases meta-analysis as topic oligonucleotide array sequence analysis

ORESTTool Content

http://mips.gsf.de/genre/proj/orest/index.html

Expression > cDNA, EST, SAGE

Online Resource for EST (OREST) analysis is a EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. Functional annotation of the dataset is also included via either FunCat or GO annotation.

NAR Web Server Issue 2008
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tagsanimals chromosome mapping dna sequence analysis expressed sequence tags fungal genes humans mammals mice proteins rats saccharomyces cerevisiae

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

ProfComTool Content

http://webclu.bio.wzw.tum.de/profcom/

Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.

NAR Web Server Issue 2008
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tagsanimals gene expression profiling genes humans mice rabbits

Human Genome > Annotations

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

SerbGOTool Content

http://www.geneontology.org/GO.tools.microarray.shtml

Human Genome > Annotations

Searching for the best GO tool (SerbGO) helps users select the GO annotation or list analysis tools which best suit their needs. SerbGO may also be used to compare the capabilities of the various GO tools in the context of the users' experiment.

NAR Web Server Issue 2008
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tagscontrolled vocabulary gene expression profiling genes genetic databases

Human Genome > Health and Disease

EpiToolKitTool Content

http://www.epitoolkit.org

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

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

GenoWatchTool Content

http://genepipe.ngc.sinica.edu.tw/genowatch

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases microsatellite repeats pubmed single nucleotide polymorphism

IEDB-ARTool Content

http://tools.immuneepitope.org

Human Genome > Health and Disease
Protein > Do-it-all Tools for Protein

The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.

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tagsb-lymphocyte epitopes factual databases histocompatibility antigens class i histocompatibility antigens class ii peptides proteins t-lymphocyte epitopes

NetMHC-3.0Tool Content

http://www.cbs.dtu.dk/services/NetMHC

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

NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.

NAR Web Server Issue 2008
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tagsalleles animals epitopes haplorhini histocompatibility antigens class i hla antigens humans mice peptides

Human Genome > Sequence Polymorphisms

EpiToolKitTool Content

http://www.epitoolkit.org

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

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

GenoWatchTool Content

http://genepipe.ngc.sinica.edu.tw/genowatch

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

NAR Web Server Issue 2008
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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases microsatellite repeats pubmed single nucleotide polymorphism

QUMATool Content

http://quma.cdb.riken.jp/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

NAR Web Server Issue 2008
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tagscpg islands dna methylation dna sequence analysis statistical data interpretation sulfites

Literature > Search Tools

soaPDBTool Content

http://soapdb.sourceforge.net/

Literature > Search Tools

soaPDB is a web application for the generation and organization of saved PDB searches as well email notifications.

NAR Web Server Issue 2008
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tagselectronic mail protein databases

Literature > Text Mining and Semantics

BioLitTool Content

http://biolit.ucsd.edu

Literature > Text Mining and Semantics

BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.

NAR Web Server Issue 2008
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tagsfactual databases protein databases pubmed systems integration

CoPubTool Content

http://www.copub.org

Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

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tagsanimals gene expression profiling humans medline mice oligonucleotide array sequence analysis rats

E3MinerTool Content

http://e3miner.biopathway.org

Literature > Text Mining and Semantics

E3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases.

NAR Web Server Issue 2008
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tagsmedline protein databases ubiquitin-protein ligases

PIETool Content

http://bi.snu.ac.kr/pie/

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

The Protein Interaction information Extraction system (PIE) is a configurable web server for extraction of protein-protein interactions from literature. Both co-occurrence of proteins in text and predefined phrase patterns for protein-protein interactions are employed in a machine learning framework.

This content is being maintained by echosf.

NAR Web Server Issue 2008
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tagsfull text protein interaction mapping protein-protein interaction sentence filtering pubmed

PolySearchTool Content

http://wishart.biology.ualberta.ca/polysearch

Literature > Text Mining and Semantics

PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.

NAR Web Server Issue 2008
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tagsalgorithms factual databases genes humans inborn genetic diseases metabolism mutation pharmaceutical preparations pubmed

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

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tagsalgorithms cluster analysis computational biology gene expression profiling

Model Organisms > General Resources

Ontology Lookup ServiceTool Content

http://www.ebi.ac.uk/ols

DNA > Annotations
DNA > DNA and Genomic Analysis
Model Organisms > General Resources

The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.

This content is being maintained by rglcote.

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tagscontrolled vocabulary database management systems factual databases natural language processing programming languages proteomics systems integration

Model Organisms > Microbes

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

NAR Web Server Issue 2008
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tagscluster analysis factual databases metabolic networks and pathways

CRISPRcomparTool Content

http://crispr.u-psud.fr/CRISPRcompar/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.

NAR Web Server Issue 2008
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tagsalleles bacteria bacterial typing techniques tandem repeat sequences

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

TargetRNATool Content

http://snowwhite.wellesley.edu/targetRNA

Model Organisms > Microbes
RNA > Functional RNAs

TargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species.

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tagsalgorithms bacterial rna base pairing genomics messenger rna rna sequence analysis untranslated rna

UM-PPSTool Content

http://umbbd.msi.umn.edu/predict/

Model Organisms > Microbes
Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.

This content is being maintained by lynda.

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tagsbiotransformation environmental pollutants factual databases

Model Organisms > Plants

GeneCATTool Content

http://genecat.mpg.de

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Plants

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

NAR Web Server Issue 2008
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tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/

Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna

Other Molecules > Compounds

SuperPredTool Content

http://bioinformatics.charite.de/superpred

Other Molecules > Compounds

The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.

This content is being maintained by robertpreissner.

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tagsbiological effect drug classification and target prediction drug design structure-activity relationship world health organization

UM-PPSTool Content

http://umbbd.msi.umn.edu/predict/

Model Organisms > Microbes
Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.

This content is being maintained by lynda.

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tagsbiotransformation environmental pollutants factual databases

Other Molecules > Metabolites

MassTRIXTool Content

http://masstrix.org

Other Molecules > Metabolites
Protein > Proteomics

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

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tagsgene expression mass spectrometry metabolic networks and pathways

Protein > 2-D Structure Prediction

Jpred 3Tool Content

http://www.compbio.dundee.ac.uk/jpred

Protein > 2-D Structure Prediction

Jpred 3 is an improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search databases.

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tagsalgorithms protein sequence analysis secondary protein structure sequence alignment

LocalMoveTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
RNA > Structure Prediction, Visualization, and Design

LocalMove is a web server for computing on-lattice fits for biopolymersusing input from PDB files for proteins or RNA molecules. Results are output in PDB file format and include a 3D movie of the intermediate conformations simulated during computation.

NAR Web Server Issue 2008
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tagsalgorithms molecular models nucleic acid conformation protein conformation rna

xREITool Content

http://biowiki.org/XreiProgram

DNA > DNA and Genomic Analysis
DNA > Gene Prediction
Protein > 2-D Structure Prediction
RNA > Functional RNAs

xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.

NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment statistical models

Protein > 3-D Structural Features

KFC ServerTool Content

http://www.mitchell-lab.org/kfc

Protein > 3-D Structural Features

The KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.

NAR Web Server Issue 2008
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tagsartificial intelligence binding sites molecular models multiprotein complexes protein conformation protein interaction mapping

MAPPISTool Content

http://bioinfo3d.cs.tau.ac.il/MAPPIS

Protein > 3-D Structural Features
Sequence Comparison > Multiple Sequence Alignments

Multiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.

NAR Web Server Issue 2008
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tagsbinding sites molecular models multiprotein complexes protein conformation protein interaction mapping

MolAxisTool Content

http://bioinfo3d.cs.tau.ac.il/MolAxis

Protein > 3-D Structural Features

The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological transport computational biology membrane proteins molecular models nucleic acids

MultiBindTool Content

http://bioinfo3d.cs.tau.ac.il/MultiBind

Protein > 3-D Structural Features
Sequence Comparison > Multiple Sequence Alignments

Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.

NAR Web Server Issue 2008
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tagsbinding sites molecular models multiprotein complexes protein conformation protein interaction mapping

Protein > 3-D Structure Comparison

3D-FunTool Content

http://3dfun.bioinfo.pl

Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

RAPIDOTool Content

http://webapps.embl-hamburg.de/rapido

Protein > 3-D Structure Comparison

RAPIDO conducts 3D alignments of crystal structures of different protein molecules in the presence of conformational change.

NAR Web Server Issue 2008
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tagsalgorithms carbon-nitrogen ligases molecular models protein structural homology tertiary protein structure

SEQATOMSTool Content

http://www.bioinformatics.nl/tools/seqatoms

Protein > 3-D Structure Comparison
Protein > Sequence Data

SEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in the BLAST output are replaced with the corresponding subsequence from the original FASTA files).

NAR Web Server Issue 2008
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tagsprotein databases protein sequence analysis sequence alignment tertiary protein structure

SuperimposeTool Content

http://bioinformatics.charite.de/superimpose

Protein > 3-D Structure Comparison

Superimpose web server performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selection of algorithms and databases that best suit their needs.

NAR Web Server Issue 2008
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tagsalgorithms binding sites factual databases molecular conformation molecular models pharmaceutical preparations protein structural homology proteins

Protein > 3-D Structure Prediction

CS23DTool Content

http://www.cs23d.ca

Protein > 3-D Structure Prediction

Chemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.

NAR Web Server Issue 2008
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tagsalgorithms biomolecular nuclear magnetic resonance protein conformation protein databases protein sequence analysis

LocalMoveTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
RNA > Structure Prediction, Visualization, and Design

LocalMove is a web server for computing on-lattice fits for biopolymersusing input from PDB files for proteins or RNA molecules. Results are output in PDB file format and include a 3D movie of the intermediate conformations simulated during computation.

NAR Web Server Issue 2008
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tagsalgorithms molecular models nucleic acid conformation protein conformation rna

Protein > 3-D Structure Retrieval/Viewing

PVSTool Content

http://imed.med.ucm.es/PVS/

Protein > 3-D Structure Retrieval/Viewing

Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.

NAR Web Server Issue 2008
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tagsaids vaccines b-lymphocyte epitopes protein conformation protein sequence analysis proteins sequence alignment t-lymphocyte epitopes viral proteins

Protein > Annotation and Function

3D-FunTool Content

http://3dfun.bioinfo.pl

Protein > 3-D Structure Comparison
Protein > Annotation and Function

3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

NAR Web Server Issue 2008
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tagsalgorithms enzymes molecular models protein structural homology

FFPredTool Content

http://bioinf.cs.ucl.ac.uk/ffpred/

Protein > Annotation and Function
Protein > Sequence Features

Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.

NAR Web Server Issue 2008
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tagsanimals humans mice protein sequence analysis proteome systems integration vertebrates

webPIPSATool Content

http://pipsa.h-its.org

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.

This content is being maintained by wade.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological models chemical models computer simulation electrostatics enzyme activation enzymes kinetics protein binding protein conformation protein interaction mapping proteins research signal transduction static electricity systems biology triose-phosphate isomerase

Protein > Biochemical Features

PBEQ-SolverTool Content

http://www.charmm-gui.org/?doc=input/pbeqsolver

Protein > Biochemical Features

PBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential.

NAR Web Server Issue 2008
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tagscell membrane dna mathematical computing molecular models protein databases proteins rna static electricity

Protein > Do-it-all Tools for Protein

IEDB-ARTool Content

http://tools.immuneepitope.org

Human Genome > Health and Disease
Protein > Do-it-all Tools for Protein

The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools.

NAR Web Server Issue 2008
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tagsb-lymphocyte epitopes factual databases histocompatibility antigens class i histocompatibility antigens class ii peptides proteins t-lymphocyte epitopes

MassNetTool Content

http://massnet.kr

Protein > Do-it-all Tools for Protein
Protein > Proteomics

MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases protein interaction mapping proteins

PROTEUS2Tool Content

http://wishart.biology.ualberta.ca/proteus2

Protein > Do-it-all Tools for Protein

PROTEUS2 is a web server for comprehensive protein structure prediction and structure-based annotation. The analysis pipeline includes signal identification, trans-membrane helix prediction, trans-membrane beta-strand prediction, secondary structure prediction and homology modeling for user inputs of single or multiple sequences.

NAR Web Server Issue 2008
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tagsalgorithms membrane proteins molecular models protein sequence analysis protein sorting signals protein structural homology secondary protein structure

Phylogeny.frTool Content

http://www.phylogeny.fr/

Protein > Do-it-all Tools for Protein
Protein > Phylogeny Reconstruction

Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation of the inferred phylogenetic tree.

NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis sequence alignment

TarOTool Content

http://www.compbio.dundee.ac.uk/taro

Protein > Do-it-all Tools for Protein

TarO is a collection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple sequence alignments and presentation of integrated results.

NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence homology protein databases protein sequence analysis proteins sequence alignment tertiary protein structure

Protein > Domains and Motifs

DHcLTool Content

http://sitron.bccs.uib.no/dhcl/

Protein > Domains and Motifs

DHcL provides analysis of the hierarchy of protein domain structures. DHcL detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.

NAR Web Server Issue 2008
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tagsmolecular models statistical data interpretation tertiary protein structure x-ray crystallography

PredikinTool Content

http://predikin.biosci.uq.edu.au

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation

NAR Web Server Issue 2008
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tagsamino acid sequence animals binding sites catalytic domain mice peptides phosphorylation protein databases protein kinases protein sequence analysis protein-serine-threonine kinases substrate specificity

WDACTool Content

http://pat.kobic.re.kr/wdac/index.htm

Protein > Domains and Motifs
Protein > Sequence Comparison

The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.

NAR Web Server Issue 2008
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tagscomputational biology protein databases protein sequence analysis protein structural homology proteins tertiary protein structure

Protein > Interactions, Pathways, Enzymes

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

NAR Web Server Issue 2008
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tagscluster analysis factual databases metabolic networks and pathways

E1DSTool Content

http://e1ds.ee.ncku.edu.tw/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

NAR Web Server Issue 2008
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tagsamino acid sequence catalytic domain conserved sequence enzymes protein sequence analysis

HubbaTool Content

http://hub.iis.sinica.edu.tw/Hubba

Protein > Interactions, Pathways, Enzymes

Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.

NAR Web Server Issue 2008
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tagsalgorithms animals fungal proteins humans mice protein interaction mapping rats

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

PIETool Content

http://bi.snu.ac.kr/pie/

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

The Protein Interaction information Extraction system (PIE) is a configurable web server for extraction of protein-protein interactions from literature. Both co-occurrence of proteins in text and predefined phrase patterns for protein-protein interactions are employed in a machine learning framework.

This content is being maintained by echosf.

NAR Web Server Issue 2008
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tagsfull text protein interaction mapping protein-protein interaction sentence filtering pubmed

PredikinTool Content

http://predikin.biosci.uq.edu.au

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation

NAR Web Server Issue 2008
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tagsamino acid sequence animals binding sites catalytic domain mice peptides phosphorylation protein databases protein kinases protein sequence analysis protein-serine-threonine kinases substrate specificity

UM-PPSTool Content

http://umbbd.msi.umn.edu/predict/

Model Organisms > Microbes
Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.

This content is being maintained by lynda.

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tagsbiotransformation environmental pollutants factual databases

Protein > Molecular Dynamics and Docking

EpiToolKitTool Content

http://www.epitoolkit.org

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

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

NAR Web Server Issue 2008
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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

FireDockTool Content

http://bioinfo3d.cs.tau.ac.il/FireDock/

Protein > Molecular Dynamics and Docking

The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.

NAR Web Server Issue 2008
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tagsalgorithms molecular models multiprotein complexes protein interaction mapping

NetMHC-3.0Tool Content

http://www.cbs.dtu.dk/services/NetMHC

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

NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.

NAR Web Server Issue 2008
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tagsalleles animals epitopes haplorhini histocompatibility antigens class i hla antigens humans mice peptides

PharmaGistTool Content

http://bioinfo3d.cs.tau.ac.il/PharmaGist

Protein > Molecular Dynamics and Docking

PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.

NAR Web Server Issue 2008
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tagsalgorithms drug design ligands molecular models pharmaceutical preparations

RosettaDock ServerTool Content

http://rosettadock.graylab.jhu.edu

Protein > Molecular Dynamics and Docking

RosettaDock server is a structure prediction program that searches the rigid body and side chain conformational space of two interacting proteins to find a minimum free-energy complex for the protein-protein interaction structure.

NAR Web Server Issue 2008
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tagsalgorithms molecular models multiprotein complexes protein conformation protein interaction mapping reproducibility of results

webPIPSATool Content

http://pipsa.h-its.org

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.

This content is being maintained by wade.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological models chemical models computer simulation electrostatics enzyme activation enzymes kinetics protein binding protein conformation protein interaction mapping proteins research signal transduction static electricity systems biology triose-phosphate isomerase

Protein > Phylogeny Reconstruction

Phylogeny.frTool Content

http://www.phylogeny.fr/

Protein > Do-it-all Tools for Protein
Protein > Phylogeny Reconstruction

Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation of the inferred phylogenetic tree.

NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis sequence alignment

Protein > Proteomics

ISPIDER CentralTool Content

http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl

Protein > Proteomics

The ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases proteomics systems integration
setsUniversity of Manchester

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MassNetTool Content

http://massnet.kr

Protein > Do-it-all Tools for Protein
Protein > Proteomics

MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases protein interaction mapping proteins

MassTRIXTool Content

http://masstrix.org

Other Molecules > Metabolites
Protein > Proteomics

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

NAR Web Server Issue 2008
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tagsgene expression mass spectrometry metabolic networks and pathways

PaLSTool Content

http://pals.bioinfo.cnio.es

Expression > Transcript Expression Analysis
Protein > Proteomics

Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.

This content is being maintained by aalibes.

NAR Web Server Issue 2008
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tagscontrolled vocabulary factual databases gene expression profiling genes metabolic networks and pathways proteins pubmed

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

Protein > Sequence Comparison

SCANPSTool Content

http://www.compbio.dundee.ac.uk/www-scanps

Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

SCANPS is a web server for iterative protein sequence database searching by dynamic programming. Sensitivity and selectivity outperform PSI-BLAST. The server allows a range of different protein sequence databases to be searched including the SCOP database of protein domains.

NAR Web Server Issue 2008
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tagsprotein databases protein sequence analysis sequence alignment tertiary protein structure

WDACTool Content

http://pat.kobic.re.kr/wdac/index.htm

Protein > Domains and Motifs
Protein > Sequence Comparison

The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.

NAR Web Server Issue 2008
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tagscomputational biology protein databases protein sequence analysis protein structural homology proteins tertiary protein structure

Protein > Sequence Data

SEQATOMSTool Content

http://www.bioinformatics.nl/tools/seqatoms

Protein > 3-D Structure Comparison
Protein > Sequence Data

SEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in the BLAST output are replaced with the corresponding subsequence from the original FASTA files).

NAR Web Server Issue 2008
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tagsprotein databases protein sequence analysis sequence alignment tertiary protein structure

Protein > Sequence Features

E1DSTool Content

http://e1ds.ee.ncku.edu.tw/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

NAR Web Server Issue 2008
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tagsamino acid sequence catalytic domain conserved sequence enzymes protein sequence analysis

FFPredTool Content

http://bioinf.cs.ucl.ac.uk/ffpred/

Protein > Annotation and Function
Protein > Sequence Features

Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.

NAR Web Server Issue 2008
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tagsanimals humans mice protein sequence analysis proteome systems integration vertebrates

Protein > Sequence Retrieval

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

RNA > Functional RNAs

MAGNOLIATool Content

http://bioinfo.lifl.fr/magnolia

RNA > Functional RNAs
Sequence Comparison > Multiple Sequence Alignments

MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.

NAR Web Server Issue 2008
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tagsalgorithms nucleic acid conformation proteins rna sequence analysis sequence alignment untranslated rna

R-CoffeeTool Content

http://www.tcoffee.org

RNA > Functional RNAs

The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.

NAR Web Server Issue 2008
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tagsalgorithms nucleic acid conformation rna sequence analysis sequence alignment untranslated rna

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

TargetRNATool Content

http://snowwhite.wellesley.edu/targetRNA

Model Organisms > Microbes
RNA > Functional RNAs

TargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species.

NAR Web Server Issue 2008
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tagsalgorithms bacterial rna base pairing genomics messenger rna rna sequence analysis untranslated rna

WARTool Content

http://genome.ku.dk/resources/war

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Webserver for Aligning structural RNAs (WAR) is a collection of methods for performing multiple alignments and secondary structure prediction for non-coding RNA sequences. The methods can be run simultaneously and a consensus prediction calculated.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/

Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

NAR Web Server Issue 2008
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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna

xREITool Content

http://biowiki.org/XreiProgram

DNA > DNA and Genomic Analysis
DNA > Gene Prediction
Protein > 2-D Structure Prediction
RNA > Functional RNAs

xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.

NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment statistical models

RNA > Motifs

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

NAR Web Server Issue 2003NAR Web Server Issue 2008NAR Web Server Issue 2011
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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

RNA > Sequence Retrieval

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

NAR Web Server Issue 2003NAR Web Server Issue 2008NAR Web Server Issue 2011
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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

RNA > Structure Prediction, Visualization, and Design

AsiDesignerTool Content

http://sysbio.kribb.re.kr/AsiDesigner/

RNA > Structure Prediction, Visualization, and Design

AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.

NAR Web Server Issue 2008
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tagsalgorithms alternative splicing messenger rna rna interference rna sequence analysis small interfering rna

IDT SciToolsTool Content

http://www.idtdna.com/SciTools/SciTools.aspx

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.

NAR Web Server Issue 2008
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tagsantisense oligonucleotides dna primers nucleic acid conformation oligonucleotide probes oligonucleotides small interfering rna

LocalMoveTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
RNA > Structure Prediction, Visualization, and Design

LocalMove is a web server for computing on-lattice fits for biopolymersusing input from PDB files for proteins or RNA molecules. Results are output in PDB file format and include a 3D movie of the intermediate conformations simulated during computation.

NAR Web Server Issue 2008
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tagsalgorithms molecular models nucleic acid conformation protein conformation rna

NOBAITool Content

http://www.manet.uiuc.edu/nobai/nobai.php

RNA > Structure Prediction, Visualization, and Design

NOBAI web server facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.

NAR Web Server Issue 2008
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OligoWalkTool Content

http://rna.urmc.rochester.edu/servers/oligowalk

RNA > Structure Prediction, Visualization, and Design

OligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides binding to a target RNA.

NAR Web Server Issue 2008
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tagsmessenger rna nucleic acid hybridization oligonucleotides rna interference rna sequence analysis small interfering rna thermodynamics

RNALogoTool Content

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

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Multiple Sequence Alignments

RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.

NAR Web Server Issue 2008
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tagsnucleic acid conformation ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment

Vienna RNA WebsuiteTool Content

http://rna.tbi.univie.ac.at/

RNA > Structure Prediction, Visualization, and Design

Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. Tools include folding of single and aligned sequences, prediction of RNA-RNA interactions, design of sequences with a given structure, analysis of folding landscapes and structural RNA alignments using LocARNA.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna rna sequence analysis sequence alignment

WARTool Content

http://genome.ku.dk/resources/war

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Webserver for Aligning structural RNAs (WAR) is a collection of methods for performing multiple alignments and secondary structure prediction for non-coding RNA sequences. The methods can be run simultaneously and a consensus prediction calculated.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

Sequence Comparison > Analysis of Aligned Sequences

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

Sequence Comparison > Comparative Genomics

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

Sequence Comparison > Multiple Sequence Alignments

MAGNOLIATool Content

http://bioinfo.lifl.fr/magnolia

RNA > Functional RNAs
Sequence Comparison > Multiple Sequence Alignments

MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.

NAR Web Server Issue 2008
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tagsalgorithms nucleic acid conformation proteins rna sequence analysis sequence alignment untranslated rna

MAPPISTool Content

http://bioinfo3d.cs.tau.ac.il/MAPPIS

Protein > 3-D Structural Features
Sequence Comparison > Multiple Sequence Alignments

Multiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.

NAR Web Server Issue 2008
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tagsbinding sites molecular models multiprotein complexes protein conformation protein interaction mapping

MultiBindTool Content

http://bioinfo3d.cs.tau.ac.il/MultiBind

Protein > 3-D Structural Features
Sequence Comparison > Multiple Sequence Alignments

Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.

NAR Web Server Issue 2008
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tagsbinding sites molecular models multiprotein complexes protein conformation protein interaction mapping

PROMALS and PROMALS3DTool Content

http://prodata.swmed.edu/promals3d

Sequence Comparison > Multiple Sequence Alignments

PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

This content is being maintained by jiminpei.

NAR Web Server Issue 2007NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence amino acid sequence homology computational biology conserved sequence molecular sequence data protein sequence analysis protein structural homology proteins reproducibility of results sensitivity and specificity sequence alignment

RNALogoTool Content

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

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Multiple Sequence Alignments

RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.

NAR Web Server Issue 2008
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tagsnucleic acid conformation ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

Sequence Comparison > Other Alignment Tools

IMGT/V-QUESTTool Content

http://imgt.cines.fr/

Sequence Comparison > Other Alignment Tools

The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.

NAR Web Server Issue 2004NAR Web Server Issue 2008
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tagsalgorithms animals b-lymphocyte gene rearrangement dna sequence analysis humans immunoglobulin fragments immunoglobulin genes immunoglobulin joining region immunoglobulin variable region mice rats sequence alignment systems integration t-lymphocyte gene rearrangement

Sequence Comparison > Pairwise Sequence Alignments

SCANPSTool Content

http://www.compbio.dundee.ac.uk/www-scanps

Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

SCANPS is a web server for iterative protein sequence database searching by dynamic programming. Sensitivity and selectivity outperform PSI-BLAST. The server allows a range of different protein sequence databases to be searched including the SCOP database of protein domains.

NAR Web Server Issue 2008
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tagsprotein databases protein sequence analysis sequence alignment tertiary protein structure

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

NAR Web Server Issue 2008
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tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

Sequence Comparison > Similarity Searching

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)