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NAR Web Server Issue 2011

RSS FeedList AlphabeticallyPublisher Site

Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Web Services

BioExtractTool Content

http://www.bioextract.org

Computer Related > Web Services
Computer Related > Workflows
DNA > DNA and Genomic Analysis

The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.

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tagsbiopolymers computational biology data mining database management systems factual databases information dissemination workflow

Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

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Computer Related > Workflows

BioExtractTool Content

http://www.bioextract.org

Computer Related > Web Services
Computer Related > Workflows
DNA > DNA and Genomic Analysis

The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.

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tagsbiopolymers computational biology data mining database management systems factual databases information dissemination workflow

MemPypeTool Content

http://mu2py.biocomp.unibo.it/mempype

Computer Related > Workflows
Protein > Localization and Targeting

MemPype is a Python-based pipeline that integrates several tools for the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

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PRI-CATTool Content

http://www.ab.wur.nl/pricat

Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

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tagsarabidopsis ChIP-seq plants transcription factors

DNA > Annotations

AnnotQTLTool Content

http://annotqtl.genouest.org

DNA > Annotations
DNA > Gene Prediction

AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

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BeeSpace NavigatorTool Content

http://www.beespace.illinois.edu

DNA > Annotations
Literature > Text Mining and Semantics

BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.

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BioPortalDatabase Content

http://bioportal.bioontology.org

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

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

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

KOBASTool Content

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

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

PHASTTool Content

http://phast.wishartlab.com/

DNA > Annotations
Model Organisms > Microbes

PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.

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antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

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g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

DNA > DNA and Genomic Analysis

BiQ Analyzer HTTool Content

http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/

DNA > DNA and Genomic Analysis

BiQ Analyzer HT Is a tool that supports locus specific analysis and visualization of high-throughput bisulfite sequencing data. It facilitates analysis of locus specific DNA methylation patterns.

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tagsdna dna methylation dna sequence analysis polymerase chain reaction sequence alignment sulfites

BioExtractTool Content

http://www.bioextract.org

Computer Related > Web Services
Computer Related > Workflows
DNA > DNA and Genomic Analysis

The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.

NAR Web Server Issue 2011
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5
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tagsbiopolymers computational biology data mining database management systems factual databases information dissemination workflow

PileLineGUITool Content

http://sing.ei.uvigo.es/pileline/pilelinegui.html

DNA > DNA and Genomic Analysis
DNA > Sequence Polymorphisms

PileLineGUI is a desktop environment for manipulating, browsing and analyzing genome position files from next generation sequencing experiments, with specific support of somatic mutation finding studies. A genome browser tool is also integrated.

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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 > Gene Prediction

AnnotQTLTool Content

http://annotqtl.genouest.org

DNA > Annotations
DNA > Gene Prediction

AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

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DNA > Mapping and Assembly

HapEditTool Content

http://embio.yonsei.ac.kr/hapedit

DNA > Mapping and Assembly

HapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.

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DNA > Phylogeny Reconstruction

PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

DNA > Sequence Polymorphisms

PileLineGUITool Content

http://sing.ei.uvigo.es/pileline/pilelinegui.html

DNA > DNA and Genomic Analysis
DNA > Sequence Polymorphisms

PileLineGUI is a desktop environment for manipulating, browsing and analyzing genome position files from next generation sequencing experiments, with specific support of somatic mutation finding studies. A genome browser tool is also integrated.

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g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

inGAP-svTool Content

http://ingap.sourceforge.net

DNA > Sequence Polymorphisms

inGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to evaluate the quality of the predicted structural variation.

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DNA > Sequence Retrieval and Submission

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

CURVES+Tool Content

http://gbio-pbil.ibcp.fr/cgi/Curves_plus/

DNA > Structure and Sequence Feature Detection

Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.

This content is being maintained by arel.

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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

DNA > Tools For the Bench

PHUSERTool Content

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

DNA > Tools For the Bench

Primer Help for Uracil Specific Exision Reagent (PHUSER) is a tool for designing primers specifically for USER fusion and USER cloning applications. Standard primer analyses are also conducted.

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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

CENTDISTTool Content

http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/

Expression > Gene Regulation

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

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ChIP-ArrayTool Content

http://wanglab.hku.hk/ChIP-Array

Expression > Gene Regulation

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

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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

DIANA-microTTool Content

http://www.microrna.gr/microT

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

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

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

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs

Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

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PRI-CATTool Content

http://www.ab.wur.nl/pricat

Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

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tagsarabidopsis ChIP-seq plants 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

ResponseNetTool Content

http://bioinfo.bgu.ac.il/respnet

Expression > Gene Regulation
Expression > Gene Set Analysis
Protein > Interactions, Pathways, Enzymes

ResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.

This content is being maintained by Esti Yeger-Lotem.

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g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

miRanalyzerTool Content

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

Expression > Gene Regulation
RNA > Functional RNAs

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

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tagsanimals dogs genetic transcription humans mice micrornas rats rna sequence analysis

miRvestigatorTool Content

http://mirvestigator.systemsbiology.net

Expression > Gene Regulation

miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).

This content is being maintained by cplaisier.

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tagsCo-expression Co-Regulation Gene Set miRNA

mirConnXTool Content

http://www.benoslab.pitt.edu/mirconnx

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Networks

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

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Expression > Gene Set Analysis

ADGOTool Content

http://www.btool.org/ADGO2

Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

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tagsalgorithms biological models computer simulation documentation gene expression profiling oligonucleotide array sequence analysis protein databases proteins

BioProfiling.deTool Content

http://www.BioProfiling.de/gene_list.

Expression > Gene Set Analysis

BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.

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PINTATool Content

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

Expression > Gene Set Analysis

PINTA is a web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA is available for 5 species (human, mouse, rat, worm and yeast).

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ResponseNetTool Content

http://bioinfo.bgu.ac.il/respnet

Expression > Gene Regulation
Expression > Gene Set Analysis
Protein > Interactions, Pathways, Enzymes

ResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.

This content is being maintained by Esti Yeger-Lotem.

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RuleGOTool Content

http://rulego.polsl.pl

Expression > Gene Set Analysis

RuleGO is a web tool for description of gene groups by means of Gene Ontology. The user is able to describe gene groups on the basis of logical rules that include GO-terms in their premises.

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SNPsynTool Content

http://snpsyn.biolab.si

Expression > Gene Set Analysis
Expression > Networks
Human Genome > Sequence Polymorphisms

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

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mirConnXTool Content

http://www.benoslab.pitt.edu/mirconnx

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Networks

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

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Expression > Networks

SNPsynTool Content

http://snpsyn.biolab.si

Expression > Gene Set Analysis
Expression > Networks
Human Genome > Sequence Polymorphisms

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

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mirConnXTool Content

http://www.benoslab.pitt.edu/mirconnx

Expression > Gene Regulation
Expression > Gene Set Analysis
Expression > Networks

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

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Expression > Transcript Expression Analysis

BioPortalDatabase Content

http://bioportal.bioontology.org

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

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

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

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

DARIOTool Content

http://dario.bioinf.uni-leipzig.de/

Expression > Transcript Expression Analysis
RNA > Functional RNAs

DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.

NAR Web Server Issue 2011
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PILGRMTool Content

http://pilgrm.princeton.edu

Expression > Transcript Expression Analysis

The Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries.

This content is being maintained by csgreene.

NAR Web Server Issue 2011
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g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

mirActTool Content

http://sysbio.ustc.edu.cn/software/mirAct

Expression > Transcript Expression Analysis
RNA > Functional RNAs

mirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.

This content is being maintained by zhouzhou.

NAR Web Server Issue 2011
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Expression > cDNA, EST, SAGE

ADGOTool Content

http://www.btool.org/ADGO2

Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

NAR Web Server Issue 2011
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tagsalgorithms biological models computer simulation documentation gene expression profiling oligonucleotide array sequence analysis protein databases proteins

Human Genome > Annotations

BioPortalDatabase Content

http://bioportal.bioontology.org

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

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

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

ncFANsTool Content

http://www.ebiomed.org/ncFANs

Human Genome > Annotations
RNA > Functional RNAs

The non-coding RNA Function ANotation server (ncFANs) is a web server for functional annotation of human and mouse long non-coding RNAs. Two strategies for lncRNA functional annotation are provided: 1) use of aspects of a coding-non-coding gene co-expression network; and 2) use of condition related differentially expressed lncRNAs.

This content is being maintained by ncfans.

NAR Web Server Issue 2011
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Human Genome > Databases

KOBASTool Content

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

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

Human Genome > Genomics

DIANA-microTTool Content

http://www.microrna.gr/microT

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

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

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

ICSNPathwayTool Content

http://icsnpathway.psych.ac.cn/

Human Genome > Genomics
Human Genome > Sequence Polymorphisms

ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.

NAR Web Server Issue 2011
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Human Genome > Sequence Polymorphisms

ICSNPathwayTool Content

http://icsnpathway.psych.ac.cn/

Human Genome > Genomics
Human Genome > Sequence Polymorphisms

ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.

NAR Web Server Issue 2011
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SNPsynTool Content

http://snpsyn.biolab.si

Expression > Gene Set Analysis
Expression > Networks
Human Genome > Sequence Polymorphisms

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

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Literature > Open Access Resources

BioPortalDatabase Content

http://bioportal.bioontology.org

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

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

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

Literature > Search Tools

BioPortalDatabase Content

http://bioportal.bioontology.org

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

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

This content is being maintained by whetzel.

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tagsbiomedical research controlled vocabulary natural language processing systems integration

Literature > Text Mining and Semantics

BeeSpace NavigatorTool Content

http://www.beespace.illinois.edu

DNA > Annotations
Literature > Text Mining and Semantics

BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.

NAR Web Server Issue 2011
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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

GénieTool Content

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

Literature > Text Mining and Semantics

Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases.

This content is being maintained by fontaine.

NAR Web Server Issue 2011
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tagsdata mining gene prioritization orthology relationships text mining

Semantic-JSONTool Content

http://semanticjson.org

Literature > Text Mining and Semantics

Semantic-JSON is an approach that provides light-weight access to Semantic Web data. It provides a Representational State Transfer (REST) Web service that retrieves Semantic Web data described in the light-weight JavaScript Object Notation (JSON) format. Semantic-JSON employs an integrated single-domain data repository, which is generated by collecting multiple-domain data on the Semantic Web.

NAR Web Server Issue 2011
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Model Organisms > Fly

DIANA-microTTool Content

http://www.microrna.gr/microT

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

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

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

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs

Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

NAR Web Server Issue 2011
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Model Organisms > Microbes

NRPSpredictor2Tool Content

http://nrps.informatik.uni-tuebingen.de/

Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity.

NAR Web Server Issue 2011
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PHASTTool Content

http://phast.wishartlab.com/

DNA > Annotations
Model Organisms > Microbes

PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.

NAR Web Server Issue 2011
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RNApredatorTool Content

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

Model Organisms > Microbes
RNA > Functional RNAs

RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.

NAR Web Server Issue 2011
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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

antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

NAR Web Server Issue 2011
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Model Organisms > Plants

PRI-CATTool Content

http://www.ab.wur.nl/pricat

Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

NAR Web Server Issue 2011
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tagsarabidopsis ChIP-seq plants transcription factors

psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/.

Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

NAR Web Server Issue 2011
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Model Organisms > Worm

DIANA-microTTool Content

http://www.microrna.gr/microT

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

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

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

Other Molecules > Compounds

ARISTOTool Content

http://www.ionspectra.org/aristo

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

NAR Web Server Issue 2011
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DRAR-CPITool Content

http://cpi.bio-x.cn/drar/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.

NAR Web Server Issue 2011
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MetalDetectorTool Content

http://metaldetector.dsi.unifi.it/v2.0/

Other Molecules > Compounds
Protein > Sequence Features

MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.

NAR Web Server Issue 2011
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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

pepMMsMIMICTool Content

http://mms.dsfarm.unipd.it/pepMMsMIMIC

Other Molecules > Compounds
Protein > 3-D Structure Comparison

pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.

This content is being maintained by matteofloris.

NAR Web Server Issue 2011
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tagschemoinformatics peptidomimetics virtual screening

Other Molecules > Metabolites

ARISTOTool Content

http://www.ionspectra.org/aristo

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

NAR Web Server Issue 2011
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GLAMMTool Content

http://glamm.lbl.gov

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

GLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.

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Other Molecules > Small Molecules

ARISTOTool Content

http://www.ionspectra.org/aristo

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

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ChemMine ToolsTool Content

http://chemmine.ucr.edu

Other Molecules > Small Molecules

ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

NAR Web Server Issue 2011
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SwissDockTool Content

http://www.swissdock.ch

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

SwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.

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Protein > 2-D Structure Prediction

PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

Protein > 3-D Structural Features

CSpritzTool Content

http://protein.bio.unipd.it/cspritz/

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

CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

This content is being maintained by silvio.tosatto@unipd.it.

NAR Web Server Issue 2011
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Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

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IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

NAR Web Server Issue 2011
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KINARI-WebTool Content

http://kinari.cs.umass.edu/

Protein > 3-D Structural Features

KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.

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PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

PhosfinderTool Content

http://phosfinder.bio.uniroma2.it

Protein > 3-D Structural Features

Phosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual display of the predicted binding sites on the query protein structure.

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SDM Tool Content

http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php

Protein > 3-D Structural Features

Site Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specific amino acid substitution frequency for homologous protein families is used to calculate a stability score.

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Protein > 3-D Structure Comparison

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click

Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

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MarkUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us

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

MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.

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T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

iPBATool Content

http://www.dsimb.inserm.fr/dsimb_tools/ipba/

Protein > 3-D Structure Comparison

iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.

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pepMMsMIMICTool Content

http://mms.dsfarm.unipd.it/pepMMsMIMIC

Other Molecules > Compounds
Protein > 3-D Structure Comparison

pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.

This content is being maintained by matteofloris.

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tagschemoinformatics peptidomimetics virtual screening

Protein > 3-D Structure Prediction

AquaSAXSTool Content

http://lorentz.dynstr.pasteur.fr/aquasaxs.php

Protein > 3-D Structure Prediction

AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.

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CSpritzTool Content

http://protein.bio.unipd.it/cspritz/

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

CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

This content is being maintained by silvio.tosatto@unipd.it.

NAR Web Server Issue 2011
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FALC-LoopTool Content

http://falc-loop.seoklab.org/

Protein > 3-D Structure Prediction

The FALC-Loop web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method.

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FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

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MultifitTool Content

http://modbase.compbio.ucsf.edu/multifit/

Protein > 3-D Structure Prediction

MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality-of-fit to the density map.

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R.E.D.Tool Content

http://q4md-forcefieldtools.org/REDS/

Protein > 3-D Structure Prediction

R.E.D. Server is designed to build force field libraries for new molecules and molecular fragments. One can derive molecular electrostatic potential-based atomic charges embedded in force field libraries for use in force field development, charge validation and molecular dynamics simulations.

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Protein > Annotation and Function

BAR-PLUSTool Content

http://bar.biocomp.unibo.it/bar2.0

Protein > Annotation and Function

BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB.

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GCViewTool Content

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

Protein > Annotation and Function

GCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.

This content is being maintained by dirk.linke and AG Linke.

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tagsamino acid sequence homology computational biology genomic context operon structure protein sequence analysis proteins sequence alignment

Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

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MarkUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us

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

MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.

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Protein > Biochemical Features

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth

Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

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PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

Protein > Domains and Motifs

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

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IntFOLDTool Content

http://www.reading.ac.uk/bioinf/IntFOLD/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

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SA-MotTool Content

http://sa-mot.mti.univ-paris-diderot.fr

Protein > Domains and Motifs

SA-Mot is a wbe server for the extraction and location of structural motifs of interest from protein loops. Recurrent and conserved structural motifs involved in structural redundancy of loops are considered.

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SLiMSearchTool Content

http://bioware.ucd.ie/slimsearch2.html

Protein > Domains and Motifs
Protein > Sequence Features

Short, Linear Motif Search (SLiMSearch) allows identification of a user defined SLiM in a proteome or set of sequences, using conservation and protein disorder context statistics to rank occurrences.

This content is being maintained by cabbagesofdoom.

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firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

Protein > Interactions, Pathways, Enzymes

DRAR-CPITool Content

http://cpi.bio-x.cn/drar/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.

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GLAMMTool Content

http://glamm.lbl.gov

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

GLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.

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GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/

Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.

This content is being maintained by alexkant.

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KOBASTool Content

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

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

NRPSpredictor2Tool Content

http://nrps.informatik.uni-tuebingen.de/

Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity.

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PAComplexTool Content

http://PAcomplex.life.nctu.edu.tw

Protein > Interactions, Pathways, Enzymes

PAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes.

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PRUNE and PROBE Tool Content

http://pallab.serc.iisc.ernet.in/probe

Protein > Interactions, Pathways, Enzymes

PRUNE is a web server for the selection of a subset of protein-protein docking poses generated during sampling search using an interface area based edge-scoring function. PROBE is a web server for refining, scoring and ranking of the resulting protein-protein docking poses using a regression model.

This content is being maintained by dpal.

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PredUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs

Protein > Interactions, Pathways, Enzymes

PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.

This content is being maintained by cliffzhang.

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tagsalgorithms binding sites computational biology molecular models multiprotein complexes protein binding protein databases protein interaction domains and motifs protein interaction mapping protein structural homology proteins surface properties systems biology

ResponseNetTool Content

http://bioinfo.bgu.ac.il/respnet

Expression > Gene Regulation
Expression > Gene Set Analysis
Protein > Interactions, Pathways, Enzymes

ResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.

This content is being maintained by Esti Yeger-Lotem.

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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

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

g:ProfilerTool Content

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

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

iPathTool Content

http://pathways.embl.de

Protein > Interactions, Pathways, Enzymes

iPath is a web tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems.

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Protein > Localization and Targeting

MemPypeTool Content

http://mu2py.biocomp.unibo.it/mempype

Computer Related > Workflows
Protein > Localization and Targeting

MemPype is a Python-based pipeline that integrates several tools for the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

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Protein > Molecular Dynamics and Docking

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth

Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

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GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/

Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.

This content is being maintained by alexkant.

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Rosetta FlexPepDockTool Content

http://flexpepdock.furmanlab.cs.huji.ac.il/

Protein > Molecular Dynamics and Docking

Rosetta FlexPepDock web server is a high resolution peptide docking protocol for modeling of peptide-protein complexes.

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SwissDockTool Content

http://www.swissdock.ch

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

SwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.

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Protein > Phylogeny Reconstruction

PhyleasProgTool Content

http://phyleasprog.inra.fr

Protein > Phylogeny Reconstruction

PhyleasProg is a web server for evolutionary analyses. Users input a list of Ensembl protein IDs and a list of species as inputs.

This content is being maintained by grpascal.

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tagsComparative genomics evolution gene multiple sequence alignement phylogenetic tree phylogeny protein structure synteny

PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

iTOLTool Content

http://itol.embl.de

Protein > Phylogeny Reconstruction

The Interactive Tree of Life (iTOL) tool is useful for the display, manipulation and annotation of phylogenetic trees. In addition to standart tree viewer functions, it offers powerful annotation of phylogenetic trees with various additional datasets. Annotated trees can be exported into various graphical formats. An user account system is provided, offering easy tree management and sharing through workspaces and projects. Programmatic access is also available.

This content is being maintained by iletunic.

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tagsalgorithms animals chromosome mapping computational biology data display decision trees genetic databases humans molecular evolution phylogeny species specificity visualization

Protein > Presentation and Format

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Protein > Sequence Comparison

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

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Protein > Sequence Features

CLIPTool Content

http://clip.med.yale.edu/selection

Protein > Sequence Features

CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.

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MetalDetectorTool Content

http://metaldetector.dsi.unifi.it/v2.0/

Other Molecules > Compounds
Protein > Sequence Features

MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.

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PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

PepServeTool Content

http://bioserver-1.bioacademy.gr/Bioserver/PepServe/

Protein > Sequence Features

PepServe is a web server for peptide analysis, clustering and visualization.

This content is being maintained by gspyrou.

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SLiMSearchTool Content

http://bioware.ucd.ie/slimsearch2.html

Protein > Domains and Motifs
Protein > Sequence Features

Short, Linear Motif Search (SLiMSearch) allows identification of a user defined SLiM in a proteome or set of sequences, using conservation and protein disorder context statistics to rank occurrences.

This content is being maintained by cabbagesofdoom.

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RNA > Functional RNAs

DARIOTool Content

http://dario.bioinf.uni-leipzig.de/

Expression > Transcript Expression Analysis
RNA > Functional RNAs

DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.

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DIANA-microTTool Content

http://www.microrna.gr/microT

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

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

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

RNApredatorTool Content

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

Model Organisms > Microbes
RNA > Functional RNAs

RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.

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corRnaTool Content

http://corrna.cs.mcgill.ca

RNA > Functional RNAs

corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.

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miRanalyzerTool Content

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

Expression > Gene Regulation
RNA > Functional RNAs

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

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tagsanimals dogs genetic transcription humans mice micrornas rats rna sequence analysis

mirActTool Content

http://sysbio.ustc.edu.cn/software/mirAct

Expression > Transcript Expression Analysis
RNA > Functional RNAs

mirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.

This content is being maintained by zhouzhou.

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ncFANsTool Content

http://www.ebiomed.org/ncFANs

Human Genome > Annotations
RNA > Functional RNAs

The non-coding RNA Function ANotation server (ncFANs) is a web server for functional annotation of human and mouse long non-coding RNAs. Two strategies for lncRNA functional annotation are provided: 1) use of aspects of a coding-non-coding gene co-expression network; and 2) use of condition related differentially expressed lncRNAs.

This content is being maintained by ncfans.

NAR Web Server Issue 2011
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psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/.

Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

NAR Web Server Issue 2011
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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.

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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

WebFR3DTool Content

http://rna.bgsu.edu/webfr3d

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFR3D is the online version of Find RNA 3D, a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate RNA 3D structural motifs such as hairpin, internal or junction loops and sarcin-ricin and kink tun internal loops.

NAR Web Server Issue 2011
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RNA > Sequence Retrieval

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

RNA > Structure Prediction, Visualization, and Design

CentroidHomfold-LASTTool Content

http://www.ncrna.org/centroidhomfold/

RNA > Structure Prediction, Visualization, and Design

CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.

NAR Web Server Issue 2011
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PETfold & PETcofoldTool Content

http://rth.dk/resources/petfold/

RNA > Structure Prediction, Visualization, and Design

The PETfold and PETcofold web servers for the analysis of multiple RNA sequences for common RNA structure and for RNA-RNA interaction sites. Analysis is based on probablistic evolutionary an thermodynamic models.

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R3D-BLASTTool Content

http://genome.cs.nthu.edu.tw/R3D-BLAST/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Similarity Searching

R3D-BLAST is a BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format; output includes a graphical display showing structural superposition.

This content is being maintained by cllu.

NAR Web Server Issue 2011
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RNAmuteTool Content

http://www.cs.bgu.ac.il/~xrnamute/XRNAmute

RNA > Structure Prediction, Visualization, and Design

RNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled.

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WebFR3DTool Content

http://rna.bgsu.edu/webfr3d

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFR3D is the online version of Find RNA 3D, a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate RNA 3D structural motifs such as hairpin, internal or junction loops and sarcin-ricin and kink tun internal loops.

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Sequence Comparison > Alignment Editing and Visualization

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Analysis of Aligned Sequences

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Comparative Genomics

CoMetTool Content

http://comet.gobics.de

Sequence Comparison > Comparative Genomics

CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.

NAR Web Server Issue 2011
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Sequence Comparison > Multiple Sequence Alignments

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

NAR Web Server Issue 2011
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PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

PicXAA-WebTool Content

http://gsp.tamu.edu/picxaa/

Sequence Comparison > Multiple Sequence Alignments

PicXAA-Web is a web tool for probablistic alignment of multiple biological sequences using probabilistic non-progressive alignment algorithms. Multiple protein, DNA and RNA sequences may be analyzed.

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T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

NAR Web Server Issue 2011
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firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

Sequence Comparison > Other Alignment Tools

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

NAR Web Server Issue 2011
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T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Pairwise Sequence Alignments

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

NAR Web Server Issue 2005NAR Web Server Issue 2011
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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

Sequence Comparison > Similarity Searching

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

NAR Web Server Issue 2011
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R3D-BLASTTool Content

http://genome.cs.nthu.edu.tw/R3D-BLAST/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Similarity Searching

R3D-BLAST is a BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format; output includes a graphical display showing structural superposition.

This content is being maintained by cllu.

NAR Web Server Issue 2011
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T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins