http://bioinformatics.ca/links_directory/journals/nar/2007http://bioinformatics.ca/links_directory/journals/nar/2007/feed en http://3d-partner.life.nctu.edu.tw/3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.9207Mon, 20 May 2013 02:40:36 -0400 http://3dlogo.uniroma2.it/3dLOGO/home.html3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.9209Tue, 21 May 2013 05:50:23 -0400 http://genome.imim.es/astalavista/AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.9250Sun, 19 May 2013 21:00:32 -0400 http://asterias.bioinfo.cnio.es/Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.9251Mon, 20 May 2013 08:10:07 -0400 http://phylogenomics.berkeley.edu/The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.9265Mon, 20 May 2013 06:50:12 -0400 http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.9270Mon, 20 May 2013 05:10:06 -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.11303Fri, 17 May 2013 20:40:27 -0400 http://oxytricha.princeton.edu/BlastO/index.htmlBLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.10407Tue, 21 May 2013 06:30:26 -0400 http://www.cgl.ucsf.edu/Research/genentech/canpredict/CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.9318Mon, 20 May 2013 05:30:21 -0400 http://cargo2.bioinfo.cnio.es/docs/aboutCargo.htmlCARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.9322Sun, 19 May 2013 16:40:08 -0400 http://digbio.missouri.edu/software/index.htmlCodonO is a method for measuring synonymous codon usage bias within and across genomes.9361Tue, 21 May 2013 00:40:08 -0400 http://prodata.swmed.edu/compass/compass.phpCOMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.9368Mon, 20 May 2013 10:00:14 -0400 http://cpc.cbi.pku.edu.cn/programs/run_cpc.jspCPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.9381Mon, 20 May 2013 19:40:11 -0400 http://crispr.u-psud.fr/Server/CRISPRfinder.phpClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.9385Tue, 21 May 2013 10:50:10 -0400 http://david.abcc.ncifcrf.gov/home.jspThe Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.10322Mon, 20 May 2013 03:10:27 -0400 http://salilab.org/DBAli/DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.9399Sun, 19 May 2013 12:30:19 -0400 http://www.bioinf.med.uni-goettingen.de/services/deep/DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).9403Mon, 20 May 2013 11:00:21 -0400 http://bioinformatics.bc.edu/clotelab/DIAL/DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.9406Thu, 16 May 2013 19:20:31 -0400 http://casp.rnet.missouri.edu/domac.htmlDOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.9425Mon, 20 May 2013 22:20:11 -0400 http://www.chem.cuhk.edu.hk/DSHIFT/DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.10376Mon, 20 May 2013 01:20:26 -0400 http://www.ebi.ac.uk/Tools/webservices/EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.10038Mon, 20 May 2013 21:30:11 -0400 http://ef-site.hgc.jp/eF-seek/index.jspeF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.10359Mon, 20 May 2013 19:50:10 -0400 http://probalign.njit.edu/probalign/logineProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.10422Tue, 21 May 2013 02:10:33 -0400 http://estexplorer.biolinfo.orgESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.10339Mon, 20 May 2013 08:20:19 -0400 http://etest.vbi.vt.edu/etblast3/eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.10750Fri, 17 May 2013 22:20:35 -0400 http://structure.pitt.edu/servers/fastcontact/FastContact is a free energy scoring tool for protein-protein complex structures.10403Sat, 18 May 2013 19:00:21 -0400 http://gemdock.life.nctu.edu.tw/fastSCOP/fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.10382Tue, 21 May 2013 05:20:17 -0400 http://www.fatigo.org/FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.9307Mon, 20 May 2013 08:10:16 -0400 http://fgf.genomics.org.cn/service/index.jspFGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).10426Sun, 19 May 2013 21:10:35 -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.10423Fri, 17 May 2013 09:40:25 -0400 http://www.flugenome.org/FluGenome is a tool for determining lineages and genotypes of influenza A viruses.10396Mon, 20 May 2013 21:40:17 -0400 http://bioserv.rpbs.jussieu.fr/cgi-bin/FrogFrog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).10386Mon, 20 May 2013 23:10:37 -0400 http://www.ogic.ca/projects/g2d_2/G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.10347Sat, 18 May 2013 10:10:36 -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.10393Sat, 18 May 2013 23:30:31 -0400 http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.10368Tue, 21 May 2013 01:00:13 -0400 http://genetrail.bioinf.uni-sb.de/index.phpGeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.10391Mon, 20 May 2013 11:40:25 -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, 21 May 2013 02:00:20 -0400 http://www.ihop-net.org/UniPub/iHOP/iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.9804Tue, 21 May 2013 09:50:16 -0400 http://indelscan.genomics.sinica.edu.tw/IndelScan/INDELSCAN is a tool for genome-wide identification of indels.10366Sun, 19 May 2013 22:10:25 -0400 http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.htmlINFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.10340Mon, 20 May 2013 01:50:32 -0400 http://biominer.bime.ntu.edu.tw/ipda/iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.10392Tue, 21 May 2013 05:40:16 -0400 http://bioinfo.cipf.es/isacghtracISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.10348Sat, 18 May 2013 01:10:53 -0400 http://www.genome.jp/kegg/kaas/KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.10360Sat, 11 May 2013 10:00:31 -0400 http://kinasephos2.mbc.nctu.edu.tw/KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.10383Sun, 19 May 2013 20:30:19 -0400 http://knots.mit.edu/KNOTS is a web server that detects knots in protein structures.10408Mon, 20 May 2013 21:50:23 -0400 http://www.lipidmaps.org/tools/index.htmlLIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.10397Thu, 09 May 2013 21:40:11 -0400 http://tlife.fudan.edu.cn/ltr_finder/LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.10330Sat, 18 May 2013 15:10:12 -0400 http://manaslu.aecom.yu.edu/M4T/M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.10335Tue, 21 May 2013 03:50:25 -0400 http://ccg.vital-it.ch/madap/MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).10394Mon, 20 May 2013 09:00:19 -0400 http://www.magma-fgcz.unizh.ch/pages/loginuser.jsfMAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.10350Fri, 17 May 2013 16:30:16 -0400 http://melina2.hgc.jp/public/index.htmlMelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.10352Tue, 21 May 2013 08:50:16 -0400 http://scopes.biologie.hu-berlin.de/MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.10355Tue, 21 May 2013 03:00:35 -0400 http://lorentz.immstr.pasteur.fr/joel/index.phpMinActionPath calculates the most-probable trajectory between two known structural states of a protein.10415Tue, 21 May 2013 08:30:16 -0400 http://www.bioinf.seu.edu.cn/miRNA/miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.10375Tue, 21 May 2013 04:20:26 -0400 http://mml.sjtu.edu.cn/MobilomeFINDER/MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.10377Fri, 17 May 2013 18:10:08 -0400 http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.htmlMODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.10395Mon, 20 May 2013 20:50:24 -0400 http://molprobity.biochem.duke.edu/MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.9882Tue, 14 May 2013 08:50:10 -0400 http://ms.iis.sinica.edu.tw/Multi-Q-Web/Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.10429Tue, 21 May 2013 01:20:31 -0400 http://www.cs.nuim.ie/distributed/multiphyl.phpMultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.10374Wed, 15 May 2013 15:00:48 -0400 http://cg1.iis.sinica.edu.tw/~mybs/index.phpMYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.10365Mon, 20 May 2013 12:40:21 -0400 http://myhits.isb-sib.chThe MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.9829Mon, 20 May 2013 12:00:27 -0400 http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgiThe NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.10421Wed, 15 May 2013 00:40:21 -0400 https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.phpNQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.10387Mon, 20 May 2013 17:10:22 -0400 http://oblab.cs.nchu.edu.tw:8080/WebSDL/NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.10373Tue, 21 May 2013 05:20:20 -0400 http://www.basic.northwestern.edu/biotools/OligoCalc.htmlOligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.10354Tue, 21 May 2013 08:30:07 -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.9912Sat, 18 May 2013 01:10:42 -0400 http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.startthis?SIMGO=w2h.welcomeOpen HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).10384Tue, 21 May 2013 07:10:18 -0400 http://www.cisreg.ca/oPOSSUM_new/oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.10310Sun, 19 May 2013 01:20:31 -0400 http://genomes.urv.es/OPTIMIZER/OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.10341Sun, 19 May 2013 09:20:15 -0400 http://biocomp.bioen.uiuc.edu/oscar/OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.10411Fri, 10 May 2013 02:50:20 -0400 http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.doPromoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.10428Mon, 20 May 2013 21:00:19 -0400 http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.10358Mon, 20 May 2013 05:00:17 -0400 http://pcons.net/Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.10336Thu, 16 May 2013 05:30:43 -0400 http://pdb2pqr.sourceforge.net/Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.9853Sun, 19 May 2013 12:40:10 -0400 http://pfp.technion.ac.il/PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.10425Mon, 20 May 2013 15:30:24 -0400 http://phobius.sbc.su.se/Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.10337Wed, 15 May 2013 01:30:31 -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, 21 May 2013 07:40:26 -0400 http://pipe.scs.fsu.edu/PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.10333Mon, 20 May 2013 18:30:26 -0400 http://crick.mbu.iisc.ernet.in/~PIC/Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.10372Mon, 20 May 2013 16:20:21 -0400 http://pknot.life.nctu.edu.tw/pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB. pKNOT-v2 has been updated with a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or PDB IDs and return knot analysis.10379Tue, 21 May 2013 07:00:12 -0400 http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.10351Sun, 19 May 2013 14:40:28 -0400 http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMGThe Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.10398Sun, 19 May 2013 09:40:17 -0400 http://prdos.hgc.jp/cgi-bin/top.cgiPrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.10371Tue, 21 May 2013 11:00:26 -0400 http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.doPrimer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.10414Sun, 19 May 2013 09:20:35 -0400 http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgiPrimer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.10380Fri, 17 May 2013 04:10:19 -0400 http://prodata.swmed.edu/promals3dPROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.10401Sun, 19 May 2013 17:40:06 -0400 http://bioportal.weizmann.ac.il/promate/ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.10342Sun, 19 May 2013 10:20:11 -0400 https://prosa.services.came.sbg.ac.at/prosa.phpProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.10388Mon, 20 May 2013 16:00:25 -0400 http://prosightptm2.scs.uiuc.edu/ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the \'Top-Down\' tandem mass spectrometry (MS/MS) approach.9914Mon, 20 May 2013 20:40:31 -0400 http://bioportal.weizmann.ac.il/dipol/The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.10381Thu, 16 May 2013 06:20:17 -0400 http://qscop-blast.services.came.sbg.ac.at/QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).10390Mon, 20 May 2013 13:10:22 -0400 http://bioinformoodics.jhmi.edu/quickSNP.plQuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.10419Fri, 17 May 2013 10:30:15 -0400 http://datalab.njit.edu/biodata/rna/RSmatch/server.htmRADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.10334Tue, 21 May 2013 08:10:16 -0400 http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.pyRCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.10410Mon, 20 May 2013 01:50:35 -0400 http://genome.cs.nthu.edu.tw/RE-MUSIC/RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression constraints.10385Tue, 21 May 2013 08:30:20 -0400 http://rocaplab.ocean.washington.edu/tools/repkREPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.10409Fri, 17 May 2013 07:40:20 -0400 http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htmRF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.10338Fri, 17 May 2013 04:40:11 -0400 http://bibiserv.techfak.uni-bielefeld.de/rnamovies/RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.10400Sat, 18 May 2013 06:10:39 -0400 http://bindr.gdcb.iastate.edu/RNABindR/RNABindR is a server for analyzing and predicting RNA binding sites in proteins.10405Sat, 18 May 2013 20:10:19 -0400 http://bioinformatics.bc.edu/clotelab/RNAbor/RNAbor is a server for computing structural neighbors of a RNA secondary structure.10412Sat, 18 May 2013 19:10:12 -0400 http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgiRNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.10345Sun, 19 May 2013 23:40:28 -0400 http://www.riboclub.org/cgi-bin/RTAnalyzer/index.pl?page=rt_findRTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.10424Mon, 20 May 2013 10:00:11 -0400 http://genie.dartmouth.edu/scope/SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.10406Mon, 20 May 2013 15:50:16 -0400 http://selecton.tau.ac.il/Selecton is a server for the identification of site-specific positive selection and purifying selection.10378Mon, 20 May 2013 19:10:29 -0400 http://fred.bioinf.uni-sb.de/sepacs.htmlSEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.10370Mon, 20 May 2013 01:30:30 -0400 http://www.ibi.vu.nl/programs/seqharmwww/Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.10389Mon, 20 May 2013 02:20:32 -0400 http://cbm.bio.uniroma2.it/SH3-Hunter/SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.10418Tue, 21 May 2013 02:00:14 -0400 http://bioware.ucd.ie/~slimdisc/SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.10413Sun, 19 May 2013 02:10:15 -0400 http://spliceport.cs.umd.edu/SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.10399Fri, 17 May 2013 13:50:30 -0400 http://www.benoslab.pitt.edu/stamp/STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.10417Mon, 20 May 2013 15:10:13 -0400 http://ilyinlab.org/StSNP/StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.10343Tue, 21 May 2013 00:40:31 -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.9642Mon, 20 May 2013 10:20:16 -0400 http://compbio.cs.sfu.ca/taverna/taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.10367Fri, 17 May 2013 17:00:23 -0400 http://tfam.lcb.uu.se/TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.10404Fri, 17 May 2013 02:50:30 -0400 http://visant.bu.edu/VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.10070Mon, 20 May 2013 21:20:08 -0400 http://genome.lbl.gov/vista/index.shtmlVISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.9635Mon, 20 May 2013 21:40:33 -0400 http://fraenkel.mit.edu/webmotifs/WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.10331Mon, 20 May 2013 10:30:21 -0400 http://www.conifergdb.org/software/wtm1.2/WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3\' and 5\' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.10363Thu, 16 May 2013 18:30:17 -0400 http://www.rothamsted.ac.uk/whets/WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.10364Sun, 19 May 2013 17:20:14 -0400 http://wolfpsort.org/WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.10353Mon, 20 May 2013 18:10:19 -0400 http://bindr.gdcb.iastate.edu/ZiFiT/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.10346Tue, 21 May 2013 10:50:19 -0400