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NAR Web Server Issue 2010

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Databases

MOWServTool Content

http://www.inab.org/MOWServ/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

MOWServ provides integrated access to databases and analytical tools. Based on the BioMoby protocol for inter-service communication.

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tagscomputational biology phylogeny protein databases proteins systems integration

TogoWSTool Content

http://togows.dbcls.jp/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.

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tagscomputational biology factual databases systems integration

Computer Related > Web Services

EMBRACE Web ServiceResource Content

http://www.embraceregistry.net

Computer Related > Web Services

European Model for Bioinformatics Research and Community Education (EMBRACE) web service consists of EDAM, an ontology for describing life sciences; BioXSD, a schema for exchanging data between services and a centralized registry of ~1000 services.

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tagsbiological science disciplines computational biology information dissemination registries systems integration

IBWS: IST Bioinformatics Web ServicesResource Content

http://bioinformatics.istge.it/ibws/

Computer Related > Web Services

The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS.

This content is being maintained by PaoloRomano.

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tagsbiological specimen banks catalogs as topic computational biology factual databases mutation nucleic acid databases p53 genes

MOWServTool Content

http://www.inab.org/MOWServ/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

MOWServ provides integrated access to databases and analytical tools. Based on the BioMoby protocol for inter-service communication.

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tagscomputational biology phylogeny protein databases proteins systems integration

Opal Web Services for Biomedical ApplicationsTool Content

http://ws.nbcr.net

Computer Related > Web Services

Opal Web Services for Biomedical Applications is a production web server. Powered by Opal, it allows users to use scientific applications easily as web services without any modification to the scientific codes.

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tagsbiomedical research computational biology database management systems

SMAP-WSTool Content

http://kryptonite.ucsd.edu/opal2/GetServicesList.do

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Proteomics

The SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.

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tagsalgorithms binding sites drug discovery ligands protein conformation protein structural homology proteome

TogoWSTool Content

http://togows.dbcls.jp/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.

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tagscomputational biology factual databases systems integration

WIWSTool Content

http://swift.cmbi.ru.nl/

Computer Related > Web Services
Protein > 3-D Structure Prediction

WHAT IF Web Services (WIWS) is a web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection has over 1600 different functions.

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tagscomputational biology molecular models protein conformation

Computer Related > Workflows

MOWServTool Content

http://www.inab.org/MOWServ/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

MOWServ provides integrated access to databases and analytical tools. Based on the BioMoby protocol for inter-service communication.

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tagscomputational biology phylogeny protein databases proteins systems integration

TogoWSTool Content

http://togows.dbcls.jp/

Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.

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tagscomputational biology factual databases systems integration

myExperimentResource Content

http://www.myexperiment.org

Computer Related > Workflows

myExperiment is an online research environment that supports the social sharing of bioinformatics workflows.

This content is being maintained by dder.

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tagscommunity networks computational biology information dissemination reproducibility of results

DNA > Annotations

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

Ontology Lookup ServiceTool Content

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

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

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

This content is being maintained by rglcote.

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

PANDORATool Content

http://www.pandora.cs.huji.ac.il

DNA > Annotations
Protein > Annotation and Function
Protein > Proteomics

The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.

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tagsanimals humans mass spectrometry mice peptides protein databases proteins proteomics rats statistical data interpretation systems integration

PhenoHMTool Content

http://phenome.cchmc.org

DNA > Annotations
Model Organisms > Mouse and Rat
Sequence Comparison > Comparative Genomics

PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.

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tagsalleles animals cataract controlled vocabulary disease gene regulatory networks genes genome humans mice phenotype

PhyloscanTool Content

http://bayesweb.wadsworth.org/phyloscan/

DNA > Annotations
Expression > Gene Regulation

Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.

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

SOBA: Sequence Ontology Bioinformatics AnalysisTool Content

http://www.sequenceontology.org/cgi-bin/soba.cgi

DNA > Annotations
Sequence Comparison > Comparative Genomics

Sequence Ontology Bioinformatics Analysis (SOBA) provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison.

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tagsgenomics sequence analysis statistical data interpretation

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

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tagsagricultural crops plant genes

DNA > DNA and Genomic Analysis

Ontology Lookup ServiceTool Content

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

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

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

This content is being maintained by rglcote.

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

DNA > Gene Prediction

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

DNA > Mapping and Assembly

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

WebPrInSeSTool Content

http://webprinses.epfl.ch/

DNA > Mapping and Assembly
DNA > Tools For the Bench

WebPrInSeS is a web server that allows automated full-length clone sequence identification and verification using high-throughput sequencing data from any of the 3 major sequencing platforms.

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tagsanimals complementary dna dna sequence analysis drosophila melanogaster high-throughput screening assays molecular cloning open reading frames

DNA > Phylogeny Reconstruction

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org

DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

SATCHMO-JSTool Content

http://phylogenomics.berkeley.edu/satchmo-js

DNA > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

SATCHMO-JS is a web server for simultaneous estimation of protein multiple sequence alignments and phylogenetic trees. Input is a FASTA file of sequences, and output is a phylogenetic tree and multiple sequence alignment.

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tagsalgorithms markov chains phylogeny protein sequence analysis sequence alignment tertiary protein structure

DNA > Sequence Polymorphisms

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

waviCGHTool Content

http://wavi.bioinfo.cnio.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

waviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.

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tagsanimals comparative genomic hybridization dna copy number variations genomics humans mice oligonucleotide array sequence analysis rats

DNA > Structure and Sequence Feature Detection

DNABINDPROTTool Content

http://www.prc.boun.edu.tr/appserv/prc/dnabindprot

DNA > Structure and Sequence Feature Detection

DNABINDPROT web tool is designed to predict DNA-binding residues in high frequency modes by the Gaussian network method.

NAR Web Server Issue 2010
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tagsbinding sites cyclic amp receptor protein dna-binding proteins

ICM WebTool Content

http://dna.ccs.tulane.edu/icm

DNA > Structure and Sequence Feature Detection

The Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.

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tagschromatin chromatin assembly and disassembly dna genetic promoter regions mouse mammary tumor virus nucleic acid conformation nucleosomes

RSSsiteTool Content

http://www.itb.cnr.it/rss

DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Model Organisms > Mouse and Rat

RSSsite consists of a reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.

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tagsalgorithms animals b-lymphocyte gene rearrangement genetic recombination genome genomics human genome humans mice nucleic acid databases nucleic acid regulatory sequences t-lymphocyte gene rearrangement

RegPredictTool Content

http://regpredict.lbl.gov

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

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

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tagsbacterial genome genomics operon regulon staphylococcaceae systems integration

SFmapTool Content

http://sfmap.technion.ac.il

DNA > Structure and Sequence Feature Detection

SFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.

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tagsalgorithms alternative splicing binding sites human genome humans rna sequence analysis rna-binding proteins

SeLOXTool Content

http://selox.mpi-cbg.de/cgi-bin/selox/index

DNA > Structure and Sequence Feature Detection

SeLOX web server identifies degenerate lox-like sites within genomic sequences.

This content is being maintained by vineeth.

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tagsbinding sites directed molecular evolution genetic recombination genomics hiv long terminal repeat human genome humans integrases inverted repeat sequences recombinases

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

THREaD Mapper StudioTool Content

http://cbr.jic.ac.uk/threadmapper

DNA > Structure and Sequence Feature Detection
Human Genome > Genomics
Model Organisms > General Resources

THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.

This content is being maintained by Jo_Dicks.

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tagschromosome mapping computational biology genetic linkage

ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

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tagsbinding sites computational biology deoxyribonucleases dna sequence analysis dna-binding proteins humans protein conformation protein engineering secondary protein structure tertiary protein structure transcription factors zinc fingers

DNA > Tools For the Bench

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

PCRTilerTool Content

http://pcrtiler.alaingervais.org:8080/PCRTiler

DNA > Tools For the Bench

PCRTiler web server tool allows for the automated design of tiled primer pairs for any number of genomic loci. Based on Primer3 and BLAST analysis for cross-hybridization.

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tagscytochrome p-450 cyp1a1 cytochrome p-450 cyp1a2 dna primers humans polymerase chain reaction

WebPrInSeSTool Content

http://webprinses.epfl.ch/

DNA > Mapping and Assembly
DNA > Tools For the Bench

WebPrInSeS is a web server that allows automated full-length clone sequence identification and verification using high-throughput sequencing data from any of the 3 major sequencing platforms.

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tagsanimals complementary dna dna sequence analysis drosophila melanogaster high-throughput screening assays molecular cloning open reading frames

chipDTool Content

http://chipd.uwbacter.org

DNA > Tools For the Bench

chipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.

This content is being maintained by ydufour.

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tagsalgorithms gene expression profiling oligonucleotide array sequence analysis oligonucleotide probes rhodobacter sphaeroides

Education > Directories and Portals

BioCatalogueResource Content

http://www.biocatalogue.org/

Education > Directories and Portals

A universal catalogue of web services for the life sciences. BioCatalogue provides a common interface for registering, browsing and annotating web services to the life science community.

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tagsbiological science disciplines catalogs as topic computational biology

Bioinformatics Links DirectoryResource Content

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

Education > Directories and Portals

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

This content is being maintained by Francis Ouellette.

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

Expression > Gene Regulation

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

PhyloscanTool Content

http://bayesweb.wadsworth.org/phyloscan/

DNA > Annotations
Expression > Gene Regulation

Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.

NAR Web Server Issue 2010
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tagsbinding sites dna sequence analysis gene expression regulation genetic promoter regions genetic transcription sequence alignment transcription factors

RegPredictTool Content

http://regpredict.lbl.gov

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

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

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tagsbacterial genome genomics operon regulon staphylococcaceae systems integration

SIREsTool Content

http://ccbg.imppc.org/sires/index.html

Expression > Gene Regulation
RNA > Motifs

SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.

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tagsalgorithms binding sites humans iron iron-regulatory proteins nucleic acid conformation ribonucleic acid regulatory sequences rna untranslated regions

SPEEDTool Content

http://speed.sys-bio.net/

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

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

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tagsalgorithms ccaat-enhancer-binding proteins gene expression profiling gene expression regulation genetic databases humans mutation myeloid leukemia signal transduction transcription factors tumor cell line

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

NAR Web Server Issue 2010
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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

TransFindTool Content

http://transfind.sys-bio.net/

Expression > Gene Regulation
Expression > Gene Set Analysis

TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.

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tagsbinding sites gene expression regulation genetic promoter regions genetic transcription phylogeny transcription factors

ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

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tagsbinding sites computational biology deoxyribonucleases dna sequence analysis dna-binding proteins humans protein conformation protein engineering secondary protein structure tertiary protein structure transcription factors zinc fingers

mirToolsTool Content

http://centre.bioinformatics.zj.cn/mirtools/

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

mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates into known miRNAs, non-coding RNA, genomic repeats, etc. among other analysis tools.

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tagsgene expression profiling high-throughput screening assays humans messenger rna rna sequence analysis

Expression > Gene Set Analysis

CCancerDatabase Content

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

Expression > Gene Set Analysis
Literature > Open Access Resources

CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

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tagsaniline compounds cell aging data mining genetic databases humans monte carlo method neoplasm genes neoplasm proteins neoplasms neoplastic gene expression regulation nitriles protein kinase inhibitors quinolines

GSA-SNPTool Content

http://gsa.muldas.org

Expression > Gene Set Analysis
Human Genome > Genomics

GSA-SNP web server performs gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.

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tagsadult body height genome-wide association study humans single nucleotide polymorphism

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

NAR Web Server Issue 2010
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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

MAGIATool Content

http://gencomp.bio.unipd.it/magia

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis
RNA > Functional RNAs

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

NAR Web Server Issue 2010
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tagsgene expression gene expression profiling gene regulatory networks humans messenger rna micrornas

MARQTool Content

http://marq.dacya.ucm.es

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

MARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.

NAR Web Server Issue 2010
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tagsanimals gene expression profiling genetic databases humans mice oligonucleotide array sequence analysis rats saccharomyces cerevisiae

PINTTool Content

http://csb2.ym.edu.tw/pint/

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

Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.

NAR Web Server Issue 2010
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tagsbiological models breast neoplasms cyclin d erbb-2 receptor female humans rac gtp-binding proteins ras proteins signal transduction

R spiderTool Content

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

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

R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.

NAR Web Server Issue 2010
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tagsgene regulatory networks genetic databases humans metabolic networks and pathways protein databases protein interaction mapping proteins signal transduction systems integration

SPEEDTool Content

http://speed.sys-bio.net/

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

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

NAR Web Server Issue 2010
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tagsalgorithms ccaat-enhancer-binding proteins gene expression profiling gene expression regulation genetic databases humans mutation myeloid leukemia signal transduction transcription factors tumor cell line

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

NAR Web Server Issue 2010
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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

Targetfinder.orgTool Content

http://targetfinder.org/

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.

NAR Web Server Issue 2010
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tagsgene expression profiling gene expression regulation genetic promoter regions oligonucleotide array sequence analysis transcription factors

ToppCluster - comparative enriched features network generator and analyzerTool Content

http://toppcluster.cchmc.org

Expression > Gene Set Analysis

ToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-associated mammalian phenotypes, promoter cis-elements, miR binding sites, etc. that are differentially represented in the gene lists can be clustered or transformed into high dimensional Cytoscape or Gephi -compatible networks.

This content is being maintained by baronow.

NAR Web Server Issue 2010
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tagsbiological systems analysis gene expression cluster analysis gene expression profiling gene regulatory networks miRNA

TransFindTool Content

http://transfind.sys-bio.net/

Expression > Gene Regulation
Expression > Gene Set Analysis

TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.

NAR Web Server Issue 2010
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tagsbinding sites gene expression regulation genetic promoter regions genetic transcription phylogeny transcription factors

Expression > Networks

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

SPEEDTool Content

http://speed.sys-bio.net/

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

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

NAR Web Server Issue 2010
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tagsalgorithms ccaat-enhancer-binding proteins gene expression profiling gene expression regulation genetic databases humans mutation myeloid leukemia signal transduction transcription factors tumor cell line

Expression > Protein Expression

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

Expression > Splicing

AltAnalyzeTool Content

http://www.altanalyze.org

Expression > Splicing

AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).

This content is being maintained by NathanSalomonis.

NAR Web Server Issue 2010
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tagsalternative splicing animals exons gene expression profiling humans mice rats

Expression > Transcript Expression Analysis

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

CLICTool Content

http://gexp2.kaist.ac.kr/clic

Expression > Transcript Expression Analysis

CLIC performs clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.

NAR Web Server Issue 2010
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tagsalgorithms cluster analysis gene expression profiling humans oligonucleotide array sequence analysis tumor cell line

DSAPTool Content

http://dsap.cgu.edu.tw

Expression > Transcript Expression Analysis
RNA > Functional RNAs

Deep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.

NAR Web Server Issue 2010
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tagsmicrornas rna sequence analysis untranslated rna

MAGIATool Content

http://gencomp.bio.unipd.it/magia

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis
RNA > Functional RNAs

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

NAR Web Server Issue 2010
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tagsgene expression gene expression profiling gene regulatory networks humans messenger rna micrornas

MARQTool Content

http://marq.dacya.ucm.es

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

MARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.

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tagsanimals gene expression profiling genetic databases humans mice oligonucleotide array sequence analysis rats saccharomyces cerevisiae

PEACETool Content

http://www.peace-tools.org

Expression > Transcript Expression Analysis

Parallel Environment for Assembly and Clustering of Gene Expression (PEACE) web tool performs high-throughput ab initio clustering of transcript fragment sequences from next-generation sequencing platforms.

NAR Web Server Issue 2010
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tagscluster analysis complementary dna dna sequence analysis gene expression profiling

SEATool Content

http://sea.bioinfo.cipf.es

Expression > Transcript Expression Analysis

Serial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data.

NAR Web Server Issue 2010
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tagsalgorithms gene expression profiling kinetics linear models oligonucleotide array sequence analysis

SPEEDTool Content

http://speed.sys-bio.net/

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

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

NAR Web Server Issue 2010
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tagsalgorithms ccaat-enhancer-binding proteins gene expression profiling gene expression regulation genetic databases humans mutation myeloid leukemia signal transduction transcription factors tumor cell line

Targetfinder.orgTool Content

http://targetfinder.org/

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.

NAR Web Server Issue 2010
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tagsgene expression profiling gene expression regulation genetic promoter regions oligonucleotide array sequence analysis transcription factors

rQuant.webTool Content

http://galaxy.fml.mpg.de

Expression > Transcript Expression Analysis

rQuant.web is a web service for quantitative analysis of RNA sequencing data based on quadratic programming. rQuant.web is available as a tool in Galaxy.

NAR Web Server Issue 2010
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tagsanimals caenorhabditis elegans gene expression profiling messenger rna rna sequence analysis

Expression > cDNA, EST, SAGE

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

Human Genome > Annotations

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

NAR Web Server Issue 2010
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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

MetaMHCTool Content

http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html

Human Genome > Annotations
Protein > Domains and Motifs
Protein > Localization and Targeting

MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.

This content is being maintained by Xihao Hu.

NAR Web Server Issue 2010
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tagsanimals binding sites histocompatibility antigens class i histocompatibility antigens class ii humans mice peptides

RSSsiteTool Content

http://www.itb.cnr.it/rss

DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Model Organisms > Mouse and Rat

RSSsite consists of a reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.

NAR Web Server Issue 2010
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tagsalgorithms animals b-lymphocyte gene rearrangement genetic recombination genome genomics human genome humans mice nucleic acid databases nucleic acid regulatory sequences t-lymphocyte gene rearrangement

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

NAR Web Server Issue 2010
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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

Human Genome > Genomics

GSA-SNPTool Content

http://gsa.muldas.org

Expression > Gene Set Analysis
Human Genome > Genomics

GSA-SNP web server performs gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.

NAR Web Server Issue 2010
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tagsadult body height genome-wide association study humans single nucleotide polymorphism

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

NAR Web Server Issue 2010
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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

THREaD Mapper StudioTool Content

http://cbr.jic.ac.uk/threadmapper

DNA > Structure and Sequence Feature Detection
Human Genome > Genomics
Model Organisms > General Resources

THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.

This content is being maintained by Jo_Dicks.

NAR Web Server Issue 2010
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tagschromosome mapping computational biology genetic linkage

i-GSEA4GWASTool Content

http://gsea4gwas.psych.ac.cn

Human Genome > Genomics
Human Genome > Sequence Polymorphisms

i-GSEA4GWAS is a web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).

NAR Web Server Issue 2010
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tagsalgorithms disease genes genome-wide association study humans single nucleotide polymorphism

mirToolsTool Content

http://centre.bioinformatics.zj.cn/mirtools/

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

mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates into known miRNAs, non-coding RNA, genomic repeats, etc. among other analysis tools.

NAR Web Server Issue 2010
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tagsgene expression profiling high-throughput screening assays humans messenger rna rna sequence analysis

Human Genome > Health and Disease

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org

DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

NAR Web Server Issue 2010
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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

SPOTTool Content

http://spot.cgsmd.isi.edu

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

The SNP Prioritization Online Tool (SPOT) is a web server for integrating biological databases into the prioritization of SNPs for further study after a genome wide association study.

NAR Web Server Issue 2010
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tagsgenetic databases genome-wide association study genomics single nucleotide polymorphism

Human Genome > Sequence Polymorphisms

MagicViewerTool Content

http://bioinformatics.zj.cn/magicviewer/

DNA > Annotations
DNA > Mapping and Assembly
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.

NAR Web Server Issue 2010
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tagsgenetic variation genomics indel mutation sequence alignment sequence analysis single nucleotide polymorphism systems integration

SPOTTool Content

http://spot.cgsmd.isi.edu

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

The SNP Prioritization Online Tool (SPOT) is a web server for integrating biological databases into the prioritization of SNPs for further study after a genome wide association study.

NAR Web Server Issue 2010
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tagsgenetic databases genome-wide association study genomics single nucleotide polymorphism

i-GSEA4GWASTool Content

http://gsea4gwas.psych.ac.cn

Human Genome > Genomics
Human Genome > Sequence Polymorphisms

i-GSEA4GWAS is a web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).

NAR Web Server Issue 2010
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tagsalgorithms disease genes genome-wide association study humans single nucleotide polymorphism

waviCGHTool Content

http://wavi.bioinfo.cnio.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

waviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.

NAR Web Server Issue 2010
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tagsanimals comparative genomic hybridization dna copy number variations genomics humans mice oligonucleotide array sequence analysis rats

Literature > Open Access Resources

CCancerDatabase Content

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

Expression > Gene Set Analysis
Literature > Open Access Resources

CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

NAR Web Server Issue 2010
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tagsaniline compounds cell aging data mining genetic databases humans monte carlo method neoplasm genes neoplasm proteins neoplasms neoplastic gene expression regulation nitriles protein kinase inhibitors quinolines

Literature > Text Mining and Semantics

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer

Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

Model Organisms > Fly

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer

Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

NAR Web Server Issue 2010
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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

NAR Web Server Issue 2010
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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

Model Organisms > General Resources

Ontology Lookup ServiceTool Content

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

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

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

This content is being maintained by rglcote.

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

THREaD Mapper StudioTool Content

http://cbr.jic.ac.uk/threadmapper

DNA > Structure and Sequence Feature Detection
Human Genome > Genomics
Model Organisms > General Resources

THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.

This content is being maintained by Jo_Dicks.

NAR Web Server Issue 2010
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tagschromosome mapping computational biology genetic linkage

Model Organisms > Microbes

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

G-language GAETool Content

http://www.g-language.org/wiki/soap/

Model Organisms > Microbes

G-language Genome Analysis Environment (G-language GAE) is a compendium of more than 100 programs that focus on bacterial genome analysis. Included are programs for identification of binding sites, analysis of codons and prediction of expression levels, analysis of nucleotide composition bias and visualization of genomic information.

This content is being maintained by gaou.

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tagsbacterial genome database management systems dna sequence analysis genome genomics nucleic acid databases sequence alignment

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org

DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

RegPredictTool Content

http://regpredict.lbl.gov

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

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

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tagsbacterial genome genomics operon regulon staphylococcaceae systems integration

mGenomeSubtractorTool Content

http://bioinfo-mml.sjtu.edu.cn/mGS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

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tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

Model Organisms > Mouse and Rat

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

PhenoHMTool Content

http://phenome.cchmc.org

DNA > Annotations
Model Organisms > Mouse and Rat
Sequence Comparison > Comparative Genomics

PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.

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tagsalleles animals cataract controlled vocabulary disease gene regulatory networks genes genome humans mice phenotype

RSSsiteTool Content

http://www.itb.cnr.it/rss

DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Model Organisms > Mouse and Rat

RSSsite consists of a reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.

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tagsalgorithms animals b-lymphocyte gene rearrangement genetic recombination genome genomics human genome humans mice nucleic acid databases nucleic acid regulatory sequences t-lymphocyte gene rearrangement

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

waviCGHTool Content

http://wavi.bioinfo.cnio.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

waviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.

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tagsanimals comparative genomic hybridization dna copy number variations genomics humans mice oligonucleotide array sequence analysis rats

Model Organisms > Other Organisms

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

Model Organisms > Other Vertebrates

TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

Model Organisms > Plants

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

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tagsagricultural crops plant genes

Model Organisms > Worm

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

Model Organisms > Yeast

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

Other Molecules > Carbohydrates

GlycoViewerTool Content

http://www.systemsbiology.org.au/glycoviewer

Other Molecules > Carbohydrates

The GlycoViewer is a web-based tool that can visualize, summarize and compare sets of gylcan structures.

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tagsglycomics glycoproteins humans neoplasms polysaccharides

Other Molecules > Compounds

Frog2Tool Content

http://bioserv.rpbs.univ-paris-diderot.fr/Frog2

Other Molecules > Compounds
Other Molecules > Small Molecules

Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

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tagsmolecular conformation molecular models pharmaceutical preparations stereoisomerism

PharmMapperTool Content

http://59.78.96.61/pharmmapper

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

PharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target.

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tagsbinding sites drug design factual databases hormonal antineoplastic agents ligands pharmaceutical preparations proteins tamoxifen

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

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tagsfactual databases isomerism metabolic networks and pathways molecular structure

e-LEA3DTool Content

http://bioinfo.ipmc.cnrs.fr/lea.html

Other Molecules > Compounds

e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.

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tagsbenzoic acid computational biology drug design ligands pharmaceutical preparations retinoic acid receptors

Other Molecules > Metabolites

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

MSEATool Content

http://www.msea.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

Metabolite Set Enrichment Analysis (MSEA) performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. MSEA uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. MSEA also facilitates conversion between metabolite common names, synonyms and other database identifies.

This content is being maintained by Jeff Xia.

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tagsanimals dictionaries as topic factual databases humans mammals metabolomics

MetExploreTool Content

http://metexplore.toulouse.inra.fr

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetExplore is a web tool that links metabolites identified in untargeted metabolomics experiments within the context of genome-scale metabolic networks. Metabolomics data is mapped onto the specific metabolic network of an organism in a interactive graphical display.

This content is being maintained by l.cottret.

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tagsgenome metabolic networks and pathways metabolomics

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

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tagsfactual databases isomerism metabolic networks and pathways molecular structure

Other Molecules > Small Molecules

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Other Molecules > Small Molecules
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

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tagsbinding sites hemoglobins ligands molecular dynamics simulation protein conformation protein structural homology

Frog2Tool Content

http://bioserv.rpbs.univ-paris-diderot.fr/Frog2

Other Molecules > Compounds
Other Molecules > Small Molecules

Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

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tagsmolecular conformation molecular models pharmaceutical preparations stereoisomerism

PharmMapperTool Content

http://59.78.96.61/pharmmapper

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

PharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target.

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tagsbinding sites drug design factual databases hormonal antineoplastic agents ligands pharmaceutical preparations proteins tamoxifen

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

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tagsfactual databases isomerism metabolic networks and pathways molecular structure

Protein > 2-D Structure Prediction

Servers at University College LondonTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

Protein > 3-D Structural Features

3DLigandSiteTool Content

http://www.sbg.bio.ic.ac.uk/3dligandsite

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

3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.

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tagsalgorithms binding sites ligands molecular models protein sequence analysis protein structural homology reproducibility of results

3VTool Content

http://3vee.molmovdb.org

Protein > 3-D Structural Features

The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.

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tagsbinding sites molecular models nucleic acid conformation protein conformation rna

ALADYNTool Content

http://aladyn.escience-lab.org

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

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.

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tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

ANCHORTool Content

http://structure.pitt.edu/anchor

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

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tagsbinding sites drug discovery multiprotein complexes protein databases protein interaction mapping

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

DBCPTool Content

http://120.107.8.16/dbcp

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

The Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.

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tagscysteine disulfides protein conformation protein folding protein sequence analysis proteins reproducibility of results

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Other Molecules > Small Molecules
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

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tagsbinding sites hemoglobins ligands molecular dynamics simulation protein conformation protein structural homology

MPlotTool Content

http://proteinformatics.charite.de/mplot/

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

MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.

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tagsmembrane proteins molecular models secondary protein structure tertiary protein structure

PCFamilyTool Content

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

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.

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tagserythropoietin erythropoietin receptors multiprotein complexes protein binding protein interaction domains and motifs protein sequence analysis protein structural homology s-phase kinase-associated proteins

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

ProBiSTool Content

http://probis.cmm.ki.si

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

Protein Binding Sites (ProBiS) is a web server which detects protein binding sites based on local structural alignments.

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tagsbinding sites heterotrimeric gtp-binding proteins protein conformation proteins

SBSPKSTool Content

http://www.nii.ac.in/sbspks.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.

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tagscatalytic domain molecular models polyketide synthases protein sequence analysis substrate specificity

SMAP-WSTool Content

http://kryptonite.ucsd.edu/opal2/GetServicesList.do

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Proteomics

The SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.

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tagsalgorithms binding sites drug discovery ligands protein conformation protein structural homology proteome

Servers at University College LondonTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

Protein > 3-D Structure Comparison

3DLigandSiteTool Content

http://www.sbg.bio.ic.ac.uk/3dligandsite

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

3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.

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tagsalgorithms binding sites ligands molecular models protein sequence analysis protein structural homology reproducibility of results

ALADYNTool Content

http://aladyn.escience-lab.org

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

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.

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tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

ConPlexTool Content

http://sbi.postech.ac.kr/ConPlex/

Protein > 3-D Structure Comparison

ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.

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tagsamino acid sequence homology molecular evolution multiprotein complexes quaternary protein structure

Dali serverDatabase Content

http://ekhidna.biocenter.helsinki.fi/dali_server

Protein > 3-D Structure Comparison

The Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.

NAR Web Server Issue 2010
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tagsbacterial proteins protein databases protein sequence analysis protein structural homology

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Other Molecules > Small Molecules
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

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tagsbinding sites hemoglobins ligands molecular dynamics simulation protein conformation protein structural homology

GISTool Content

http://agknapp.chemie.fu-berlin.de/gplus

Protein > 3-D Structure Comparison

GIS (Gangsta+ internet services) allows users to analyze protein structure families according to the SCOP classification scheme. Users can upload their own protein structures for pair-wise protein structure comparison, structure alignment or symmetry analysis.

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tagsalgorithms protein databases protein structural homology tertiary protein structure

PCFamilyTool Content

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

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.

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tagserythropoietin erythropoietin receptors multiprotein complexes protein binding protein interaction domains and motifs protein sequence analysis protein structural homology s-phase kinase-associated proteins

ProBiSTool Content

http://probis.cmm.ki.si

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

Protein Binding Sites (ProBiS) is a web server which detects protein binding sites based on local structural alignments.

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tagsbinding sites heterotrimeric gtp-binding proteins protein conformation proteins

ProteinDBSTool Content

http://proteindbs.rnet.missouri.edu/

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

ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.

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tagsdatabase management systems molecular models protein conformation protein databases reproducibility of results tertiary protein structure time factors

SMAP-WSTool Content

http://kryptonite.ucsd.edu/opal2/GetServicesList.do

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Proteomics

The SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.

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tagsalgorithms binding sites drug discovery ligands protein conformation protein structural homology proteome

deconSTRUCTDatabase Content

http://epsf.bmad.bii.a-star.edu.sg/struct_server.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction

deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.

This content is being maintained by ivanam.

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tagsalgorithms binding sites databases fold similariy molecular models protein databases protein structural homology protein structure comparison proteins secondary protein structure sub-structure

Protein > 3-D Structure Prediction

CPHmodels-3.0Tool Content

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

Protein > 3-D Structure Prediction

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling.

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tagsalgorithms protein folding protein sequence analysis protein structural homology reproducibility of results

DBCPTool Content

http://120.107.8.16/dbcp

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

The Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.

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tagscysteine disulfides protein conformation protein folding protein sequence analysis proteins reproducibility of results

FoXSTool Content

http://salilab.org/foxs

Protein > 3-D Structure Prediction

Fast X-ray Scattering (FoXS) is a web server for computing the small angle x-ray scattering (SAXS) structure profile of a molecule in solution and for comparing the computed profile to the experimental profile.

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tagssmall angle scattering x-ray diffraction

MPlotTool Content

http://proteinformatics.charite.de/mplot/

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

MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.

NAR Web Server Issue 2010
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tagsmembrane proteins molecular models secondary protein structure tertiary protein structure

NMR Constraints AnalyserTool Content

http://molsim.sci.univr.it/constraint

Protein > 3-D Structure Prediction

NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.

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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation

PROSESS: A Protein Structure Evaluation Suite and ServerTool Content

http://www.prosess.ca

Protein > 3-D Structure Prediction

PROSESS (PROtein Structure Evaluation Suite and Server) is a comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.

NAR Web Server Issue 2010
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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation x-ray crystallography

PUDGETool Content

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

Protein > 3-D Structure Prediction

PUDGE is a protein structure prediction server. Modeling is divided into 5 stages: template selection, alignment, model building, model refinement and model evaluation.

NAR Web Server Issue 2010
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tagsbacterial proteins molecular models protein structural homology

RosettaBackrubTool Content

http://kortemmelab.ucsf.edu/backrub

Protein > 3-D Structure Prediction

The RosettaBackrub server computes near-native conformational ensembles from a single input protein structure in PDB format using the Backrub method.

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tagsmolecular models point mutation protein conformation protein interaction mapping protein sequence analysis proteins

SBSPKSTool Content

http://www.nii.ac.in/sbspks.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.

NAR Web Server Issue 2010
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tagscatalytic domain molecular models polyketide synthases protein sequence analysis substrate specificity

SMOG@ctbpTool Content

http://smog.ucsd.edu

Protein > 3-D Structure Prediction

SMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials.

This content is being maintained by smogatctbp.

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tagsdna molecular dynamics simulation protein folding proteins rna

Servers at University College LondonTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

WIWSTool Content

http://swift.cmbi.ru.nl/

Computer Related > Web Services
Protein > 3-D Structure Prediction

WHAT IF Web Services (WIWS) is a web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection has over 1600 different functions.

NAR Web Server Issue 2010
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tagscomputational biology molecular models protein conformation

deconSTRUCTDatabase Content

http://epsf.bmad.bii.a-star.edu.sg/struct_server.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction

deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.

This content is being maintained by ivanam.

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tagsalgorithms binding sites databases fold similariy molecular models protein databases protein structural homology protein structure comparison proteins secondary protein structure sub-structure

Protein > 3-D Structure Retrieval/Viewing

GRAPE: GRaphical Abstracted Protein ExplorerTool Content

http://grape.uwbacter.org

Protein > 3-D Structure Retrieval/Viewing

GRaphical Abstracted Protein Explorer (GRAPE) is a web server that allows users to explore abstracted representations of proteins. Large scale structural features are preserved while other surfaces are effectively reduced.

NAR Web Server Issue 2010
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tagsmolecular models protein conformation

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

NAR Web Server Issue 2010
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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

ProteinDBSTool Content

http://proteindbs.rnet.missouri.edu/

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

ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.

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tagsdatabase management systems molecular models protein conformation protein databases reproducibility of results tertiary protein structure time factors

Protein > Annotation and Function

MuDDatabase Content

http://MuD.tau.ac.il

Protein > Annotation and Function

Mutation Detector (MuD) is a web server uses structural and sequence derived features to assess the impact of a given substitution on the protein function.

NAR Web Server Issue 2010
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tagsalgorithms amino acid sequence homology amino acid substitution artificial intelligence protein conformation reproducibility of results

PANDORATool Content

http://www.pandora.cs.huji.ac.il

DNA > Annotations
Protein > Annotation and Function
Protein > Proteomics

The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.

NAR Web Server Issue 2010
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tagsanimals humans mass spectrometry mice peptides protein databases proteins proteomics rats statistical data interpretation systems integration

PCFamilyTool Content

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

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.

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tagserythropoietin erythropoietin receptors multiprotein complexes protein binding protein interaction domains and motifs protein sequence analysis protein structural homology s-phase kinase-associated proteins

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

NAR Web Server Issue 2010
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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

Protein > Domains and Motifs

MetaMHCTool Content

http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html

Human Genome > Annotations
Protein > Domains and Motifs
Protein > Localization and Targeting

MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.

This content is being maintained by Xihao Hu.

NAR Web Server Issue 2010
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tagsanimals binding sites histocompatibility antigens class i histocompatibility antigens class ii humans mice peptides

SLiMFinderTool Content

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

Protein > Domains and Motifs

SLiMFinder web server is a de novo motif discovery tool for short linear motifs (SLiMs). Statistically over represented motifs within a set of protein sequences are identified and scored. Users have numerous masking options to control the contextual information to be analyzed.

NAR Web Server Issue 2010
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tagsalgorithms amino acid motifs protein sequence analysis sequence alignment

Servers at University College LondonTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

Protein > Interactions, Pathways, Enzymes

ANCHORTool Content

http://structure.pitt.edu/anchor

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

NAR Web Server Issue 2010
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tagsbinding sites drug discovery multiprotein complexes protein databases protein interaction mapping

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet

Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

NAR Web Server Issue 2010
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tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

DrugScorePPITool Content

http://cpclab.uni-duesseldorf.de/dsppi

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.

NAR Web Server Issue 2010
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tagsalanine multiprotein complexes mutation protein interaction mapping ral gtp-binding proteins ral guanine nucleotide exchange factor

HotPointTool Content

http://prism.ccbb.ku.edu.tr/hotpoint

Protein > Interactions, Pathways, Enzymes

HotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface; output includes an interactive 3D visualization of the hot spots.

NAR Web Server Issue 2010
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tagsbinding sites interleukin-2 interleukin-2 receptors multiprotein complexes protein interaction mapping

MSEATool Content

http://www.msea.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

Metabolite Set Enrichment Analysis (MSEA) performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. MSEA uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. MSEA also facilitates conversion between metabolite common names, synonyms and other database identifies.

This content is being maintained by Jeff Xia.

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tagsanimals dictionaries as topic factual databases humans mammals metabolomics

MetExploreTool Content

http://metexplore.toulouse.inra.fr

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetExplore is a web tool that links metabolites identified in untargeted metabolomics experiments within the context of genome-scale metabolic networks. Metabolomics data is mapped onto the specific metabolic network of an organism in a interactive graphical display.

This content is being maintained by l.cottret.

NAR Web Server Issue 2010
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tagsgenome metabolic networks and pathways metabolomics

PCFamilyTool Content

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

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.

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tagserythropoietin erythropoietin receptors multiprotein complexes protein binding protein interaction domains and motifs protein sequence analysis protein structural homology s-phase kinase-associated proteins

PINTTool Content

http://csb2.ym.edu.tw/pint/

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

Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.

NAR Web Server Issue 2010
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tagsbiological models breast neoplasms cyclin d erbb-2 receptor female humans rac gtp-binding proteins ras proteins signal transduction

PathPredTool Content

http://www.genome.jp/tools/pathpred/

Protein > Interactions, Pathways, Enzymes

PathPred is an enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pathways of environmental compounds and biosynthesis pathways of secondary metabolites are predicted.

NAR Web Server Issue 2010
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tagsbiocatalysis biosynthetic pathways environmental pollutants enzymes metabolic networks and pathways

PharmMapperTool Content

http://59.78.96.61/pharmmapper

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

PharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target.

NAR Web Server Issue 2010
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tagsbinding sites drug design factual databases hormonal antineoplastic agents ligands pharmaceutical preparations proteins tamoxifen

R spiderTool Content

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

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

R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.

NAR Web Server Issue 2010
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tagsgene regulatory networks genetic databases humans metabolic networks and pathways protein databases protein interaction mapping proteins signal transduction systems integration

SBSPKSTool Content

http://www.nii.ac.in/sbspks.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.

NAR Web Server Issue 2010
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tagscatalytic domain molecular models polyketide synthases protein sequence analysis substrate specificity

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

NAR Web Server Issue 2010
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tagsfactual databases isomerism metabolic networks and pathways molecular structure

Struct2NetTool Content

http://struct2net.csail.mit.edu

Protein > Interactions, Pathways, Enzymes

Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure based approach.

This content is being maintained by dkp.

NAR Web Server Issue 2010
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tagsboosting interaction prediction interface threading logistic regression protein complex protein data bank protein protein interactions protein threading

VISIBIOwebTool Content

http://visibioweb.patika.org

Protein > Interactions, Pathways, Enzymes

VISIBIOweb is a web-based pathway visualization and layout service for pathway models in BioPAX format. Models are based on the Systems Biology Graphical Notation and pathway object properties such as external database references, may be inspected interactively.

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tagsbiological models

Protein > Localization and Targeting

MetaMHCTool Content

http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html

Human Genome > Annotations
Protein > Domains and Motifs
Protein > Localization and Targeting

MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.

This content is being maintained by Xihao Hu.

NAR Web Server Issue 2010
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tagsanimals binding sites histocompatibility antigens class i histocompatibility antigens class ii humans mice peptides

Servers at University College LondonTool Content

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

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

YLocTool Content

http://www.multiloc.org/YLoc

Protein > Localization and Targeting

YLoc is a web server for the prediction of subcellular localization. Predictions are explained and biological properties used for the prediction highlighted. In addition, a confidence estimates rates the reliability of individual predictions.

This content is being maintained by sebastian_v_b.

NAR Web Server Issue 2010
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tagsanimals fungal proteins organelles plant proteins protein sequence analysis proteins reproducibility of results

Protein > Molecular Dynamics and Docking

3DLigandSiteTool Content

http://www.sbg.bio.ic.ac.uk/3dligandsite

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

3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.

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tagsalgorithms binding sites ligands molecular models protein sequence analysis protein structural homology reproducibility of results

FiberDockTool Content

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

Protein > Molecular Dynamics and Docking

FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.

NAR Web Server Issue 2010
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tagsalgorithms molecular models multiprotein complexes protein conformation protein interaction mapping

HexServerTool Content

http://hexserver.loria.fr/

Protein > Molecular Dynamics and Docking

A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.

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tagsalgorithms binding sites multiprotein complexes protein conformation

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

NAR Web Server Issue 2010
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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

ParticleStatsTool Content

http://www.ParticleStats.com

Protein > Molecular Dynamics and Docking

ParticleStats is a web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects.

This content is being maintained by rshamilton.

NAR Web Server Issue 2010
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tagschromosome segregation kinetochores microtubules motion

SiMMapTool Content

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

Protein > Molecular Dynamics and Docking

The SiMMap server statistically derives site-moiety maps which describe the relationship between moiety preferences and the physico-chemical properties of the binding site. Users input the interaction profiles of a query target protein and its docked compound.

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tagsbinding sites drug discovery estrogen receptors ligands proteins thymidine kinase

Protein > Proteomics

PANDORATool Content

http://www.pandora.cs.huji.ac.il

DNA > Annotations
Protein > Annotation and Function
Protein > Proteomics

The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.

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tagsanimals humans mass spectrometry mice peptides protein databases proteins proteomics rats statistical data interpretation systems integration

SMAP-WSTool Content

http://kryptonite.ucsd.edu/opal2/GetServicesList.do

Computer Related > Web Services
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Proteomics

The SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.

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tagsalgorithms binding sites drug discovery ligands protein conformation protein structural homology proteome

Protein > Sequence Comparison

Multi-HarmonyTool Content

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

Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

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tagsalgorithms protein sequence analysis sequence alignment smad proteins

Protein > Sequence Features

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

DrugScorePPITool Content

http://cpclab.uni-duesseldorf.de/dsppi

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.

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tagsalanine multiprotein complexes mutation protein interaction mapping ral gtp-binding proteins ral guanine nucleotide exchange factor

Multi-HarmonyTool Content

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

Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

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tagsalgorithms protein sequence analysis sequence alignment smad proteins

NAPSTool Content

http://proteomics.bioengr.uic.edu/NAPS

Protein > Sequence Features

NAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.

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tagsalgorithms binding sites dna-binding proteins protein sequence analysis reproducibility of results rna-binding proteins

PiRaNhATool Content

http://www.bioinformatics.sussex.ac.uk/PIRANHA

Protein > Sequence Features

The PiRaNhA web server predicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.

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tagsalgorithms artificial intelligence binding sites computational biology protein databases protein sequence analysis rna rna-binding proteins

RNA > Functional RNAs

DSAPTool Content

http://dsap.cgu.edu.tw

Expression > Transcript Expression Analysis
RNA > Functional RNAs

Deep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.

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tagsmicrornas rna sequence analysis untranslated rna

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

RNA > Functional RNAs
RNA > General Resources
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

NAR Web Server Issue 2010
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tagsmessenger rna nucleic acid conformation rna rna sequence analysis sequence alignment systems integration untranslated rna

MAGIATool Content

http://gencomp.bio.unipd.it/magia

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis
RNA > Functional RNAs

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

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tagsgene expression gene expression profiling gene regulatory networks humans messenger rna micrornas

PLAST-ncRNATool Content

http://plastrna.njit.edu

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments

PLAST-ncRNA is an online tool for aligning distantly similar non-coding RNA sequences to a genome using the Probalign program. Useful for detection of potential homologous ncRNA sequences in large genomes.

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tagsalgorithms nucleic acid sequence homology rna sequence analysis sequence alignment untranslated rna

mirToolsTool Content

http://centre.bioinformatics.zj.cn/mirtools/

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

mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates into known miRNAs, non-coding RNA, genomic repeats, etc. among other analysis tools.

NAR Web Server Issue 2010
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tagsgene expression profiling high-throughput screening assays humans messenger rna rna sequence analysis

RNA > General Resources

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

RNA > Functional RNAs
RNA > General Resources
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

NAR Web Server Issue 2010
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tagsmessenger rna nucleic acid conformation rna rna sequence analysis sequence alignment systems integration untranslated rna

RNA > Motifs

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

RNA > Functional RNAs
RNA > General Resources
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

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tagsmessenger rna nucleic acid conformation rna rna sequence analysis sequence alignment systems integration untranslated rna

SIREsTool Content

http://ccbg.imppc.org/sires/index.html

Expression > Gene Regulation
RNA > Motifs

SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.

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tagsalgorithms binding sites humans iron iron-regulatory proteins nucleic acid conformation ribonucleic acid regulatory sequences rna untranslated regions

RNA > Structure Prediction, Visualization, and Design

CyloFoldTool Content

http://cylofold.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design

CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.

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tagsalgorithms nucleic acid conformation rna rna sequence analysis

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

Sequence Comparison > Alignment Editing and Visualization

EMBL-EBI FrameworkTool Content

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

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

NAR Web Server Issue 2010
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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

TranslatorXTool Content

http://translatorx.co.uk

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

TranslatorX is a web-server designed to align protein coding nucleotide sequences based on their corresponding amino acid translations rather than nucleotide alignments.

This content is being maintained by fabascal.

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tagsdna sequence analysis genetic code phylogeny protein biosynthesis protein sequence analysis sequence alignment

Sequence Comparison > Analysis of Aligned Sequences

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

EMBL-EBI FrameworkTool Content

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

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

Sequence Comparison > Comparative Genomics

PhenoHMTool Content

http://phenome.cchmc.org

DNA > Annotations
Model Organisms > Mouse and Rat
Sequence Comparison > Comparative Genomics

PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.

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tagsalleles animals cataract controlled vocabulary disease gene regulatory networks genes genome humans mice phenotype

RegPredictTool Content

http://regpredict.lbl.gov

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

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

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tagsbacterial genome genomics operon regulon staphylococcaceae systems integration

SOBA: Sequence Ontology Bioinformatics AnalysisTool Content

http://www.sequenceontology.org/cgi-bin/soba.cgi

DNA > Annotations
Sequence Comparison > Comparative Genomics

Sequence Ontology Bioinformatics Analysis (SOBA) provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison.

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tagsgenomics sequence analysis statistical data interpretation

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

NAR Web Server Issue 2010
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tagsagricultural crops plant genes

mGenomeSubtractorTool Content

http://bioinfo-mml.sjtu.edu.cn/mGS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

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tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

Sequence Comparison > Multiple Sequence Alignments

ALTERTool Content

http://sing.ei.uvigo.es/ALTER/

Sequence Comparison > Multiple Sequence Alignments

ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.

This content is being maintained by lipido.

NAR Web Server Issue 2010
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tagsdna sequence analysis protein sequence analysis sequence alignment

DIALIGN-TXTool Content

http://dialign-tx.gobics.de/

Sequence Comparison > Multiple Sequence Alignments

DIALIGN-TX is an update to DIALIGN. It combines the greedy heuristic method of DIALIGN with a traditional progressive method.

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tagsprotein sequence analysis secondary protein structure sequence alignment

EMBL-EBI FrameworkTool Content

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

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

RNA > Functional RNAs
RNA > General Resources
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

NAR Web Server Issue 2010
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tagsmessenger rna nucleic acid conformation rna rna sequence analysis sequence alignment systems integration untranslated rna

GUIDANCETool Content

http://guidance.tau.ac.il

Sequence Comparison > Multiple Sequence Alignments

The GUIDANCE web server assesses alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences; output is a graphic visualization of the alignment with confidence scores at each residue.

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tagshuman immunodeficiency virus proteins protein sequence analysis sequence alignment viral regulatory and accessory proteins

Multi-HarmonyTool Content

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

Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

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tagsalgorithms protein sequence analysis sequence alignment smad proteins

SATCHMO-JSTool Content

http://phylogenomics.berkeley.edu/satchmo-js

DNA > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

SATCHMO-JS is a web server for simultaneous estimation of protein multiple sequence alignments and phylogenetic trees. Input is a FASTA file of sequences, and output is a phylogenetic tree and multiple sequence alignment.

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tagsalgorithms markov chains phylogeny protein sequence analysis sequence alignment tertiary protein structure

TranslatorXTool Content

http://translatorx.co.uk

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

TranslatorX is a web-server designed to align protein coding nucleotide sequences based on their corresponding amino acid translations rather than nucleotide alignments.

This content is being maintained by fabascal.

NAR Web Server Issue 2010
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tagsdna sequence analysis genetic code phylogeny protein biosynthesis protein sequence analysis sequence alignment

Sequence Comparison > Pairwise Sequence Alignments

PLAST-ncRNATool Content

http://plastrna.njit.edu

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments

PLAST-ncRNA is an online tool for aligning distantly similar non-coding RNA sequences to a genome using the Probalign program. Useful for detection of potential homologous ncRNA sequences in large genomes.

NAR Web Server Issue 2010
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tagsalgorithms nucleic acid sequence homology rna sequence analysis sequence alignment untranslated rna

Sequence Comparison > Similarity Searching

EMBL-EBI FrameworkTool Content

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

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

NAR Web Server Issue 2010
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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis