http://www.bioinformatics.ca/links_directory/journals/nar/2011http://www.bioinformatics.ca/links_directory/journals/nar/2011/feed en http://www.btool.org/ADGO2ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.12158Wed, 16 May 2012 19:20:08 -0400 http://annotqtl.genouest.orgAnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.12157Mon, 14 May 2012 04:10:04 -0400 http://antismash.secondarymetabolites.orgThe antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. 12211Mon, 07 May 2012 04:50:06 -0400 http://lorentz.dynstr.pasteur.fr/aquasaxs.phpAquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.12179Sun, 13 May 2012 20:50:11 -0400 http://www.ionspectra.org/aristoAutomatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum. 12156Sun, 13 May 2012 20:10:10 -0400 http://bar.biocomp.unibo.it/bar2.0BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB.12155Wed, 16 May 2012 14:10:05 -0400 http://www.beespace.illinois.eduBeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.12154Thu, 10 May 2012 12:40:05 -0400 http://www.bioextract.orgThe BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.12153Tue, 15 May 2012 13:30:11 -0400 http://www.bioinformatics.ca/links_directory/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.11303Mon, 07 May 2012 01:10:05 -0400 http://bioportal.bioontology.orgBioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.9288Wed, 16 May 2012 17:40:13 -0400 http://www.BioProfiling.de/gene_list.BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.12152Tue, 15 May 2012 19:40:05 -0400 http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/BiQ Analyzer HT Is a tool that supports locus specific analysis and visualization of high-throughput bisulfite sequencing data. It facilitates analysis of locus specific DNA methylation patterns.12151Sat, 12 May 2012 16:40:12 -0400 http://compbio.ddns.comp.nus.edu.sg/~chipseq/centdist/CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks. 12150Wed, 16 May 2012 03:30:05 -0400 http://www.ncrna.org/centroidhomfold/CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.12149Wed, 16 May 2012 09:20:08 -0400 http://chemmine.ucr.eduChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.12148Mon, 14 May 2012 14:40:12 -0400 http://wanglab.hku.hk/ChIP-ArrayChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.12147Wed, 16 May 2012 02:40:08 -0400 http://mspc.bii.a-star.edu.sg/clickCLICK web server is a topology independent method of comparison of biomolecular 3D structures.12146Wed, 16 May 2012 17:20:06 -0400 http://clip.med.yale.edu/selectionCLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.12145Mon, 27 Jun 2011 16:50:44 -0400 http://comet.gobics.deCoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.12144Mon, 27 Jun 2011 16:50:53 -0400 http://bioit.dmbr.ugent.be/ConTra/index.phpThe Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcription factor binding sites predicted using TransFac, JASPAR or PWM libraries on aligned promoter sequences. Nine reference organisms are supported for analysis of promoter regions, 5' UTRs, 3' UTRs and introns.9375Sat, 12 May 2012 16:20:04 -0400 http://www.copub.orgCoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.9377Mon, 14 May 2012 21:00:13 -0400 http://corrna.cs.mcgill.cacorRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.12143Wed, 16 May 2012 06:00:16 -0400 http://protein.bio.unipd.it/cspritz/CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.12142Mon, 14 May 2012 23:30:08 -0400 http://gbio-pbil.ibcp.fr/cgi/Curves_plus/Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.12141Sun, 13 May 2012 20:20:07 -0400 http://dario.bioinf.uni-leipzig.de/DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.12140Mon, 27 Jun 2011 16:50:51 -0400 http://mspc.bii.a-star.edu.sg/depthDEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.12139Mon, 14 May 2012 04:50:16 -0400 http://www.microrna.gr/microTThe DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.9409Thu, 17 May 2012 00:20:13 -0400 http://cpi.bio-x.cn/drar/DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome. 12138Mon, 27 Jun 2011 16:50:54 -0400 http://falc-loop.seoklab.org/The FALC-Loop web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method.12137Sat, 12 May 2012 10:10:12 -0400 http://ffas.godziklab.orgThe Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.10009Tue, 15 May 2012 08:10:11 -0400 http://firedb.bioinfo.cnio.es/Php/FireStar.phpFirestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.10423Tue, 15 May 2012 17:00:11 -0400 http://biit.cs.ut.ee/gprofiler/g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.10393Sun, 13 May 2012 09:10:07 -0400 http://toolkit.tuebingen.mpg.de/gcviewGCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.12136Wed, 16 May 2012 15:30:10 -0400 http://gene3d.biochem.ucl.ac.uk/WebServices/The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.12180Wed, 16 May 2012 18:30:11 -0400 http://cbdm.mdc-berlin.de/tools/genie/Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases. 12159Tue, 15 May 2012 21:10:37 -0400 http://veda.cs.uiuc.edu/gsGenome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser. 12134Thu, 17 May 2012 02:50:20 -0400 http://glamm.lbl.govGLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.12181Mon, 14 May 2012 17:40:06 -0400 http://gpudock.orgchm.bas.bg/Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.12133Sun, 13 May 2012 11:30:09 -0400 http://embio.yonsei.ac.kr/hapeditHapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.12132Mon, 27 Jun 2011 16:50:55 -0400 http://hmmer.janelia.orgHMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.12131Wed, 16 May 2012 12:50:07 -0400 http://icsnpathway.psych.ac.cn/ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.12130Tue, 15 May 2012 23:00:08 -0400 http://ingap.sourceforge.netinGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to evaluate the quality of the predicted structural variation.12233Wed, 16 May 2012 15:40:13 -0400 http://www.reading.ac.uk/bioinf/IntFOLD/The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.12129Mon, 14 May 2012 22:20:10 -0400 http://pathways.embl.deiPath is a web tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems.12128Wed, 16 May 2012 14:50:10 -0400 http://www.dsimb.inserm.fr/dsimb_tools/ipba/iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.12127Wed, 16 May 2012 10:40:17 -0400 http://itol.embl.deThe Interactive Tree of Life (iTOL) tool is useful for the display, manipulation and annotation of phylogenetic trees. In addition to standart tree viewer functions, it offers powerful annotation of phylogenetic trees with various additional datasets. Annotated trees can be exported into various graphical formats. An user account system is provided, offering easy tree management and sharing through workspaces and projects. Programmatic access is also available.12182Tue, 15 May 2012 16:10:09 -0400 http://kinari.cs.umass.edu/KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.12212Thu, 10 May 2012 12:20:07 -0400 http://kobas.cbi.pku.edu.cnKEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).10231Sat, 12 May 2012 13:50:09 -0400 http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-UsMarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.12213Tue, 15 May 2012 04:30:06 -0400 http://mu2py.biocomp.unibo.it/mempypeMemPype is a Python-based pipeline that integrates several tools for the prediction of topology and subcellular localization of Eukaryotic membrane proteins.12126Thu, 17 May 2012 01:10:07 -0400 http://metaldetector.dsi.unifi.it/v2.0/MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.12125Fri, 11 May 2012 11:20:05 -0400 http://sysbio.ustc.edu.cn/software/mirActmirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.12053Sun, 13 May 2012 05:50:09 -0400 http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.10593Wed, 16 May 2012 18:10:04 -0400 http://www.benoslab.pitt.edu/mirconnxmirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.12124Tue, 08 May 2012 01:00:27 -0400 http://mirvestigator.systemsbiology.netmiRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).12123Wed, 16 May 2012 14:40:15 -0400 http://modbase.compbio.ucsf.edu/multifit/MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality-of-fit to the density map.12232Sat, 12 May 2012 03:00:04 -0400 http://www.ebiomed.org/ncFANsThe non-coding RNA Function ANotation server (ncFANs) is a web server for functional annotation of human and mouse long non-coding RNAs. Two strategies for lncRNA functional annotation are provided: 1) use of aspects of a coding-non-coding gene co-expression network; and 2) use of condition related differentially expressed lncRNAs.12183Thu, 30 Jun 2011 21:40:06 -0400 http://nrps.informatik.uni-tuebingen.de/NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity. 12184Mon, 27 Jun 2011 16:50:57 -0400 http://PAcomplex.life.nctu.edu.twPAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes.12185Wed, 16 May 2012 11:40:10 -0400 http://mms.dsfarm.unipd.it/pepMMsMIMICpepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.12122Wed, 16 May 2012 10:30:18 -0400 http://bioserver-1.bioacademy.gr/Bioserver/PepServe/PepServe is a web server for peptide analysis, clustering and visualization. 12121Tue, 15 May 2012 07:50:05 -0400 http://rth.dk/resources/petfold/The PETfold and PETcofold web servers for the analysis of multiple RNA sequences for common RNA structure and for RNA-RNA interaction sites. Analysis is based on probablistic evolutionary an thermodynamic models. 12120Wed, 16 May 2012 08:30:06 -0400 http://phast.wishartlab.com/PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.12231Sun, 13 May 2012 20:20:08 -0400 http://phosfinder.bio.uniroma2.itPhosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual display of the predicted binding sites on the query protein structure.12119Mon, 14 May 2012 20:10:14 -0400 http://www.cbs.dtu.dk/services/phuser/Primer Help for Uracil Specific Exision Reagent (PHUSER) is a tool for designing primers specifically for USER fusion and USER cloning applications. Standard primer analyses are also conducted.12118Mon, 14 May 2012 10:10:12 -0400 http://phyleasprog.inra.frPhyleasProg is a web server for evolutionary analyses. Users input a list of Ensembl protein IDs and a list of species as inputs.12117Tue, 15 May 2012 15:50:17 -0400 http://phylemon.bioinfo.cipf.esPhylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.10349Tue, 15 May 2012 18:20:06 -0400 http://gsp.tamu.edu/picxaa/PicXAA-Web is a web tool for probablistic alignment of multiple biological sequences using probabilistic non-progressive alignment algorithms. Multiple protein, DNA and RNA sequences may be analyzed.12116Sun, 13 May 2012 15:50:08 -0400 http://sing.ei.uvigo.es/pileline/pilelinegui.htmlPileLineGUI is a desktop environment for manipulating, browsing and analyzing genome position files from next generation sequencing experiments, with specific support of somatic mutation finding studies. A genome browser tool is also integrated.12186Sun, 13 May 2012 21:20:08 -0400 http://pilgrm.princeton.eduThe Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries.12187Mon, 14 May 2012 22:30:11 -0400 http://www.esat.kuleuven.be/pinta/PINTA is a web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA is available for 5 species (human, mouse, rat, worm and yeast).12115Wed, 16 May 2012 20:50:11 -0400 http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUsPredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.12114Wed, 16 May 2012 07:30:06 -0400 http://www.ab.wur.nl/pricatPRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY. 12113Wed, 16 May 2012 18:00:10 -0400 http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgiProtein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.10281Sun, 13 May 2012 00:50:05 -0400 http://pallab.serc.iisc.ernet.in/probePRUNE is a web server for the selection of a subset of protein-protein docking poses generated during sampling search using an interface area based edge-scoring function. PROBE is a web server for refining, scoring and ranking of the resulting protein-protein docking poses using a regression model.12112Sat, 12 May 2012 23:50:14 -0400 http://plantgrn.noble.org/psRNATarget/.psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.12111Wed, 16 May 2012 08:00:05 -0400 http://q4md-forcefieldtools.org/REDS/R.E.D. Server is designed to build force field libraries for new molecules and molecular fragments. One can derive molecular electrostatic potential-based atomic charges embedded in force field libraries for use in force field development, charge validation and molecular dynamics simulations.12110Tue, 15 May 2012 19:10:11 -0400 http://genome.cs.nthu.edu.tw/R3D-BLAST/R3D-BLAST is a BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format; output includes a graphical display showing structural superposition.12109Tue, 15 May 2012 23:00:06 -0400 http://bioinfo.bgu.ac.il/respnetResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.12188Sun, 03 Jul 2011 08:57:09 -0400 http://www.cs.bgu.ac.il/~xrnamute/XRNAmuteRNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled.12214Wed, 16 May 2012 09:00:07 -0400 http://rna.tbi.univie.ac.at/RNApredatorRNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.12215Thu, 17 May 2012 03:00:09 -0400 http://flexpepdock.furmanlab.cs.huji.ac.il/Rosetta FlexPepDock web server is a high resolution peptide docking protocol for modeling of peptide-protein complexes. 12189Sat, 12 May 2012 16:50:06 -0400 http://rsat.ccb.sickkids.ca/Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.10112Tue, 15 May 2012 21:20:05 -0400 http://rulego.polsl.plRuleGO is a web tool for description of gene groups by means of Gene Ontology. The user is able to describe gene groups on the basis of logical rules that include GO-terms in their premises.12234Wed, 16 May 2012 20:20:15 -0400 http://sa-mot.mti.univ-paris-diderot.frSA-Mot is a wbe server for the extraction and location of structural motifs of interest from protein loops. Recurrent and conserved structural motifs involved in structural redundancy of loops are considered.12190Tue, 15 May 2012 21:00:04 -0400 http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.phpSite Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specific amino acid substitution frequency for homologous protein families is used to calculate a stability score.12191Wed, 16 May 2012 13:00:08 -0400 http://semanticjson.orgSemantic-JSON is an approach that provides light-weight access to Semantic Web data. It provides a Representational State Transfer (REST) Web service that retrieves Semantic Web data described in the light-weight JavaScript Object Notation (JSON) format. Semantic-JSON employs an integrated single-domain data repository, which is generated by collecting multiple-domain data on the Semantic Web. 12192Wed, 16 May 2012 17:30:10 -0400 http://bioware.ucd.ie/slimsearch2.htmlShort, Linear Motif Search (SLiMSearch) allows identification of a user defined SLiM in a proteome or set of sequences, using conservation and protein disorder context statistics to rank occurrences. 12193Sun, 13 May 2012 18:20:03 -0400 http://snpsyn.biolab.siSNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.12194Thu, 17 May 2012 01:20:04 -0400 http://www.swissdock.chSwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.12195Fri, 11 May 2012 01:30:05 -0400 http://www.tcoffee.org/The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.9642Tue, 15 May 2012 02:10:06 -0400 http://umbbd.msi.umn.edu/predict/The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.10485Fri, 11 May 2012 18:10:07 -0400 http://rna.bgsu.edu/webfr3dWebFR3D is the online version of Find RNA 3D, a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate RNA 3D structural motifs such as hairpin, internal or junction loops and sarcin-ricin and kink tun internal loops.12196Sun, 13 May 2012 06:20:08 -0400