http://www.bioinformatics.ca/links_directory/journals/nar/2003http://www.bioinformatics.ca/links_directory/journals/nar/2003/feed en http://motif.stanford.edu/distributions/3matrix/3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.9211Mon, 14 May 2012 04:00:10 -0400 http://motif.stanford.edu/distributions/3motif/3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.9212Thu, 17 May 2012 01:40:19 -0400 http://www.wdcm.org/AHMII/ahmii.htmlAgent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.10142Wed, 16 May 2012 08:30:17 -0400 http://alggen.lsi.upc.es/ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.10122Wed, 16 May 2012 22:50:15 -0400 http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.phpAnnotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.9230Wed, 16 May 2012 19:20:13 -0400 http://salilab.org/our_resources.shtmlThis page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).11316Thu, 17 May 2012 00:40:06 -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://bioverse.compbio.washington.edu/Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.10003Tue, 15 May 2012 16:40:08 -0400 http://blast2srs.embl.de/BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.10157Thu, 17 May 2012 01:50:08 -0400 http://sts.bioengr.uic.edu/castp/Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.9326Sat, 12 May 2012 13:30:09 -0400 http://genomics.bioen.illinois.edu/chipinfo/ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.9345Mon, 14 May 2012 00:50:04 -0400 http://www.ebi.ac.uk/clustalw/Standard multiple sequence alignment.9353Sat, 12 May 2012 18:20:10 -0400 http://zlab.bu.edu/cluster-buster/Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.9355Mon, 14 May 2012 16:30:23 -0400 http://blocks.fhcrc.org/codehop.htmlCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.9360Sun, 13 May 2012 11:50:07 -0400 http://fasta.bioch.virginia.edu/crp/Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.9387Wed, 16 May 2012 14:40:12 -0400 http://biocore.unl.edu/primer/primerPI.htmlDesign Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.10148Mon, 14 May 2012 22:20:08 -0400 http://bioapp.psych.uic.edu/DNannotator.htmDNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).10144Tue, 15 May 2012 17:10:07 -0400 http://cubic.bioc.columbia.edu/services/DSSPcont/DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.10101Fri, 11 May 2012 09:40:07 -0400 http://elm.eu.org/Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.9733Wed, 16 May 2012 10:40:16 -0400 http://espript.ibcp.fr/ESPript/ENDscript/index.phpENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.10151Sun, 13 May 2012 09:20:07 -0400 http://enterix.cbcb.umd.edu/EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.10167Mon, 14 May 2012 14:20:08 -0400 http://rulai.cshl.edu/tools/ESE/ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.10174Wed, 16 May 2012 18:10:10 -0400 http://espript.ibcp.fr/ESPript/ESPript/index.phpEasy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.10152Wed, 16 May 2012 23:00:26 -0400 http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.plEUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.10146Wed, 16 May 2012 06:30:05 -0400 http://cubic.bioc.columbia.edu/eva/EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.9490Thu, 17 May 2012 03:00:21 -0400 http://www.expasy.org/Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.10754Mon, 14 May 2012 22:20:08 -0400 http://array.mbb.yale.edu/analysis/ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.10141Tue, 15 May 2012 12:40:14 -0400 http://genopole.toulouse.inra.fr/bioinfo/FrameD/FDFrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.10145Mon, 14 May 2012 17:50:08 -0400 http://pbga.pasteur.fr/GeneFizz/GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.10181Tue, 15 May 2012 04:40:08 -0400 http://www.cbs.dtu.dk/services/GenePublisherGenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.10140Mon, 14 May 2012 17:00:16 -0400 http://www.plantgdb.org/search/misc/PublicPlantSeq.phpGeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.10113Wed, 16 May 2012 05:40:06 -0400 http://www.geno2pheno.org/cgi-bin/geno2pheno.plGeno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.10182Sat, 12 May 2012 06:40:06 -0400 http://www.gepas.orgThe Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.9917Wed, 16 May 2012 08:50:06 -0400 http://ccmbweb.ccv.brown.edu/gibbs/gibbs.htmlGibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).9746Tue, 15 May 2012 09:20:10 -0400 http://globplot.embl.de/GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.9732Mon, 07 May 2012 01:00:07 -0400 http://goblet.molgen.mpg.de/GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.9909Thu, 10 May 2012 09:00:09 -0400 http://cbcsrv.watson.ibm.com/Tspd.htmlExtensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.9845Mon, 14 May 2012 09:50:06 -0400 http://www.esat.kuleuven.ac.be/inclusiveINCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.10138Wed, 16 May 2012 17:00:08 -0400 http://cbm.bio.uniroma2.it/ispot/iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.10130Thu, 17 May 2012 03:00:23 -0400 http://www.jvirgel.de/JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.10184Mon, 14 May 2012 05:50:11 -0400 http://cubic.bioc.columbia.edu/db/LOC3d/LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.11435Wed, 16 May 2012 19:40:05 -0400 http://www.gene-regulation.com/pub/programs.html#matchMatch is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.10176Wed, 16 May 2012 17:10:11 -0400 http://strcomp.protein.osaka-u.ac.jp/matras/MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.10109Tue, 15 May 2012 14:40:04 -0400 http://mfold.rna.albany.edu/?q=mfold/download-mfoldPredict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.9644Mon, 14 May 2012 08:00:09 -0400 http://salilab.org/modeller/Homology or comparative modeling of 3D protein structures.9748Sat, 12 May 2012 06:40:04 -0400 http://projects.villa-bosch.de/dbase/molsurfer/Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.10107Tue, 15 May 2012 08:50:19 -0400 http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.htmlMotif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.10104Mon, 14 May 2012 05:40:07 -0400 http://bioinfo.lifl.fr/mreps/mreps is a tool for identifing tandemn repeats in DNA sequences.10125Wed, 16 May 2012 02:40:13 -0400 http://ndbserver.rutgers.edu/services/The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.10220Wed, 16 May 2012 05:20:05 -0400 http://tools.neb.com/NEBcutter/index.php3NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.9623Tue, 15 May 2012 05:10:13 -0400 http://www.ebi.ac.uk/newt/displayNEWT is the taxonomy database maintained by the UniProt group.11437Wed, 16 May 2012 19:30:06 -0400 http://cubic.bioc.columbia.edu/services/NORSp/NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.10178Wed, 16 May 2012 15:30:06 -0400 http://www.receptors.org/NR/servers/html/Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.10132Sat, 12 May 2012 13:20:10 -0400 http://www.cbs.dtu.dk/services/OligoWiz2/OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.10017Tue, 15 May 2012 15:50:04 -0400 http://vortex.cs.wayne.edu/Projects.htmlOnto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.9912Wed, 16 May 2012 09:00:09 -0400 http://www.proweb.org/parsesnp/Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.10158Wed, 16 May 2012 21:40:08 -0400 http://pbil.univ-lyon1.fr/Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.10131Sun, 13 May 2012 22:30:07 -0400 http://dbb.nhri.org.tw/primer/Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.10147Wed, 16 May 2012 10:30:04 -0400 http://www.daimi.au.dk/~compbio/pfoldThe Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.10137Wed, 16 May 2012 15:20:06 -0400 http://igs-server.cnrs-mrs.fr/phydbac/Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.9830Sat, 12 May 2012 03:20:04 -0400 http://www.russell.embl.de/pints/Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.10106Mon, 14 May 2012 19:30:10 -0400 http://bips.u-strasbg.fr/PipeAlign/PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.10177Tue, 15 May 2012 18:50:09 -0400 http://bio.cse.psu.edu/PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.9706Sun, 13 May 2012 14:00:09 -0400 http://mathbio.nimr.mrc.ac.uk/wiki/POPSParameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.10121Mon, 14 May 2012 06:50:05 -0400 http://www.predictprotein.orgPredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.9828Tue, 15 May 2012 05:40:07 -0400 http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promoterPromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.10170Tue, 15 May 2012 12:20:06 -0400 http://biowulf.bu.edu/zlab/PromoSer/Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.9854Wed, 16 May 2012 03:10:04 -0400 http://protinfo.compbio.washington.edu/Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.10043Wed, 16 May 2012 21:20:09 -0400 http://pseudoviewer.inha.ac.kr/PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.10135Tue, 15 May 2012 12:40:19 -0400 http://www.psort.org/PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.9473Wed, 16 May 2012 17:30:12 -0400 http://icb.med.cornell.edu/crt/RbDe/index.xmlResidue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.10183Mon, 14 May 2012 05:40:08 -0400 http://bussemaker.bio.columbia.edu/reduce/REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.10143Wed, 16 May 2012 12:10:12 -0400 http://www.cbs.dtu.dk/services/RevTrans/RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.10169Sat, 12 May 2012 19:00:04 -0400 http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).10164Wed, 16 May 2012 21:50:14 -0400 http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.10139Thu, 17 May 2012 01:40:03 -0400 http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.htmlRNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.10154Wed, 16 May 2012 17:30:13 -0400 http://www.rnasoft.ca/Software for RNA/DNA secondary structure prediction and design9760Wed, 16 May 2012 11:30:16 -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://scansite.mit.edu/Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.10123Mon, 07 May 2012 17:40:04 -0400 http://www.nii.res.in/searchpks.htmlSEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.10120Wed, 16 May 2012 21:30:07 -0400 http://dicsoft2.physics.iisc.ernet.in/sem/Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.10108Wed, 16 May 2012 00:40:07 -0400 http://blocks.fhcrc.org/sift/SIFT.htmlSorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.10159Wed, 16 May 2012 05:50:12 -0400 http://sirw.embl.de/SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.10150Wed, 16 May 2012 11:50:09 -0400 http://rocky.bms.umist.ac.uk/SiteSeer/SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.10175Wed, 16 May 2012 15:30:12 -0400 http://stat.genopole.cnrs.fr/spatt/index.htmlStatistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.10126Tue, 15 May 2012 11:40:05 -0400 http://www.isrec.isb-sib.ch/ssa/Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).10116Wed, 16 May 2012 18:50:07 -0400 http://cluster.physics.iisc.ernet.in/ssep/options.htmlSecondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.10134Mon, 14 May 2012 23:10:09 -0400 http://luna.bioc.columbia.edu/SMS/STINGm/STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.10042Wed, 16 May 2012 05:00:21 -0400 http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgiSupport Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.10129Mon, 14 May 2012 04:00:09 -0400 http://www.ch.embnet.org/Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.10153Tue, 15 May 2012 07:50:04 -0400 http://www.expasy.ch/swissmod/SWISS-MODEL.htmlAutomated protein modelling server.9486Tue, 15 May 2012 12:50:06 -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://luna.bioc.columbia.edu/Target_Explorer/Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.10186Mon, 14 May 2012 13:20:11 -0400 http://mendel.imp.ac.at/The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.10118Wed, 16 May 2012 09:40:09 -0400 http://www.tigr.org/software/A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).11293Wed, 16 May 2012 13:20:04 -0400 http://cubic.bioc.columbia.edu/services/tmh_benchmark/The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.10119Mon, 14 May 2012 08:10:10 -0400 http://bioportal.weizmann.ac.il/tracts/tracts.htmlTRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.10127Wed, 16 May 2012 22:30:05 -0400 http://cubic.bioc.columbia.edu/services/uniqueprot/UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.10156Wed, 16 May 2012 20:50:04 -0400 http://redpoll.pharmacy.ualberta.ca/vadar/Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.10102Tue, 15 May 2012 18:50:14 -0400 http://www.tbi.univie.ac.at/~ivo/RNA/Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.9606Tue, 15 May 2012 20:20:13 -0400 http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.10160Wed, 16 May 2012 20:50:09 -0400 http://feature.stanford.edu/webfeature/WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.10103Tue, 15 May 2012 06:20:11 -0400 http://www.xml.nig.ac.jp/index.htmlXML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.10179Wed, 16 May 2012 21:00:42 -0400 http://www.ogic.ca/projects/xplormed/XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.10185Tue, 15 May 2012 05:10:12 -0400 http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.plYMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.10091Wed, 16 May 2012 06:20:06 -0400