http://www.bioinformatics.ca/links_directory/journals/nar/2006http://www.bioinformatics.ca/links_directory/journals/nar/2006/feed en http://ps2.life.nctu.edu.tw(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.12580Mon, 14 May 2012 09:00:15 -0400 http://cluster.physics.iisc.ernet.in/3dss/options.html3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.9210Fri, 11 May 2012 06:10:09 -0400 http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.phpArabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.9216Wed, 16 May 2012 13:20:07 -0400 http://www.imtech.res.in/raghava/algpred/AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.9221Mon, 14 May 2012 08:30:13 -0400 http://bioinfow.dep.usal.es/apid/Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.9233Tue, 15 May 2012 00:10:09 -0400 http://manaslu.aecom.yu.edu/loopred/ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.9236Thu, 17 May 2012 02:10:09 -0400 http://bioinfo3d.cs.tau.ac.il/ARTS/Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.9243Wed, 16 May 2012 22:10:13 -0400 http://t.caspur.it/ASPIC/Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.9249Thu, 17 May 2012 02:20:06 -0400 http://bioinf.uni-greifswald.de/augustusAUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.9254Tue, 15 May 2012 01:30:08 -0400 http://www.babelomics.orgBabelomics 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.9257Wed, 16 May 2012 07:00:05 -0400 http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.phpBActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.9256Wed, 16 May 2012 16:40:26 -0400 http://bioinformatics.ksu.edu/bindn/BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).10279Tue, 15 May 2012 13:10:13 -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://brak.sdsc.edu/pub/BiologicalNetworks/BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.10284Mon, 14 May 2012 21:30:08 -0400 http://www.ncbi.nlm.nih.gov/BLAST/Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.9622Tue, 15 May 2012 06:50:07 -0400 http://botdb.abcc.ncifcrf.gov/botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.9310Wed, 16 May 2012 15:20:07 -0400 http://bioinformatics.bc.edu/clotelab/BTW/Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.9315Mon, 14 May 2012 22:30:11 -0400 http://bioinfo.curie.fr/CAPweb/CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.9320Fri, 11 May 2012 03:10:19 -0400 https://carmaweb.genome.tugraz.at/carma/Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.9321Thu, 17 May 2012 00:00:26 -0400 http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.htmlCascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).9324Wed, 02 May 2012 23:30:19 -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://ceas.cbi.pku.edu.cnCis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.9336Wed, 16 May 2012 17:40:05 -0400 http://www.gene-regulation.com/pub/programs/cma/CMA.htmlComposite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.9356Mon, 14 May 2012 20:30:04 -0400 http://corgen.molgen.mpg.deCorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.9378Wed, 16 May 2012 06:30:07 -0400 http://correlogo.abcc.ncifcrf.gov/CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.9379Tue, 15 May 2012 02:40:14 -0400 http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.htmlCrosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.9386Sun, 13 May 2012 04:40:10 -0400 http://140.120.213.10:8080/crsd/main/home.jspComposite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).9388Sun, 13 May 2012 23:00:05 -0400 http://cupsat.uni-koeln.de/Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.9391Wed, 16 May 2012 16:00:06 -0400 http://bioinformatics.bc.edu/clotelab/DiANNA/DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.9410Wed, 16 May 2012 09:50:07 -0400 http://dilimot.embl.de/Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.9412Sun, 13 May 2012 11:10:05 -0400 http://disulfind.dsi.unifi.it/DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.9419Tue, 15 May 2012 16:20:11 -0400 http://mendel.imp.ac.at/dout/Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.9427Sat, 12 May 2012 01:40:06 -0400 http://miracle.igib.res.in/dynavac/DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.10259Tue, 15 May 2012 05:00:12 -0400 http://egassembler.hgc.jpEGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.10215Wed, 16 May 2012 04:50:11 -0400 http://bioserv.rpbs.jussieu.fr/Help/FAFDrugs.htmlFree ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.10208Wed, 16 May 2012 14:10:13 -0400 http://fastsnp.ibms.sinica.edu.twFunction Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.10250Sat, 12 May 2012 08:00:22 -0400 http://www.cbs.dtu.dk/services/FeatureMap3D/FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.10243Thu, 17 May 2012 01:00:33 -0400 http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.plFeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.10304Wed, 16 May 2012 20:40:07 -0400 http://max.ucmp.umu.se/sahmm/Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.10299Tue, 15 May 2012 03:10:11 -0400 http://psfs.cbrc.jp/fold-rate/FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.10192Tue, 15 May 2012 00:00:08 -0400 http://tubic.tju.edu.cn/GC-Profile/GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.10194Wed, 16 May 2012 18:50:08 -0400 http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/mainGeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.10226Wed, 16 May 2012 13:10:12 -0400 http://darwin.uvigo.es/software/gendecoder.htmlGenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.10196Tue, 08 May 2012 02:20:12 -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://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimationGlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.10267Wed, 16 May 2012 10:50:17 -0400 http://vakser.bioinformatics.ku.edu/resources/gramm/grammxGRAMM-X is a protein docking server.10274Tue, 15 May 2012 04:30:09 -0400 http://caps.ncbs.res.in/harmony/Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.10287Tue, 15 May 2012 11:50:04 -0400 http://toolkit.tuebingen.mpg.de/hhrepHHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).10302Mon, 14 May 2012 12:20:07 -0400 http://toolkit.tuebingen.mpg.de/hhsenserHHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.10303Wed, 16 May 2012 03:40:06 -0400 http://www.hubmed.org/HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.10189Mon, 14 May 2012 06:10:09 -0400 http://210.212.215.199/icr/index.htmlIdentify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.10227Mon, 14 May 2012 08:10:10 -0400 http://its2.bioapps.biozentrum.uni-wuerzburg.de/The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.10290Mon, 14 May 2012 14:50:10 -0400 http://jphmm.gobics.de/Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.10257Mon, 14 May 2012 13:10:06 -0400 http://bibiserv.techfak.uni-bielefeld.de/jpredictor/jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.10251Thu, 17 May 2012 01:30:18 -0400 http://www.jprogo.de/index.jspJProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.10298Sun, 13 May 2012 12:20:13 -0400 http://msa.cgb.ki.se/cgi-bin/msa.cgiKalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.10222Fri, 11 May 2012 23:30:07 -0400 http://abcis.cbs.cnrs.fr/kindock/KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).10240Wed, 16 May 2012 06:20:05 -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://localodom.kobic.re.kr/LocaloDom/Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.10308Tue, 15 May 2012 07:40:09 -0400 http://biominer.bime.ntu.edu.tw/magiicpro/MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.10283Wed, 16 May 2012 05:00:06 -0400 http://meme.nbcr.net/meme/intro.htmlThe MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.10615Wed, 16 May 2012 18:30:04 -0400 http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.htmlMethylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).10255Wed, 16 May 2012 16:40:28 -0400 http://bioinformatics.leeds.ac.uk/shark/Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.10225Mon, 14 May 2012 13:40:05 -0400 http://bio.cs.washington.edu/MicroFootPrinter.htmlMicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.10216Wed, 16 May 2012 04:30:05 -0400 http://www.migenas.org/Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.10256Wed, 16 May 2012 15:00:04 -0400 http://159.149.109.16/modtools/Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.10295Wed, 16 May 2012 12:10:12 -0400 http://darwin.uvigo.es/software/modeltest_server.htmlModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.10191Tue, 15 May 2012 09:40:09 -0400 http://prix.uos.ac.kr/research.jspModi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.10262Wed, 16 May 2012 17:20:05 -0400 http://toolkit.tuebingen.mpg.deMax-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.10242Fri, 11 May 2012 21:10:14 -0400 http://bioinfo.bsd.uchicago.edu/MutScreener.htmlMutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.10230Thu, 17 May 2012 01:00:04 -0400 http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgiNearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.10261Thu, 10 May 2012 21:00:09 -0400 http://neuroproteomics.scs.uiuc.edu/neuropred.htmlNeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.10272Wed, 16 May 2012 23:30:05 -0400 http://lorentz.immstr.pasteur.fr/nomad-ref.phpNormal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.10213Wed, 16 May 2012 14:30:30 -0400 http://www.sfu.ca/~ibajic/NXSensor/Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.10115Tue, 15 May 2012 13:40:10 -0400 http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htmOnline Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.10218Tue, 15 May 2012 07:50:09 -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://opaas.ibms.sinica.edu.tw/Optimal, Permuted, and Other Alternative Alignments of Protein Structures (OPAAS) is a tool for investigating structural neighbors that can calculate a structural alignment for two protein structures.10265Wed, 09 May 2012 20:10:10 -0400 http://coot.embl.de/pal2nal/PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.10288Wed, 16 May 2012 14:20:04 -0400 http://www.pantherdb.org/tools/The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.10246Tue, 15 May 2012 05:20:14 -0400 http://past.in.tum.de/Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids.10270Sat, 05 May 2012 22:10:15 -0400 http://bioinformatics.univ-reunion.fr/PBE/Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.10266Sat, 12 May 2012 15:20:12 -0400 http://pda.uab.es/pda2/PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.9823Tue, 15 May 2012 08:00:15 -0400 http://lorentz.immstr.pasteur.fr/solvate_mutate.phpPDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.10217Wed, 16 May 2012 18:30:07 -0400 http://pheps.orgchm.bas.bg/home.htmlpH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.10229Sun, 13 May 2012 04:10:04 -0400 http://repeats.abc.hu/cgi-bin/plotrep.plPlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output.10264Tue, 15 May 2012 06:40:05 -0400 http://pongo.biocomp.unibo.it/PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.10238Wed, 16 May 2012 12:10:04 -0400 http://www.bioinfo.biocenter.helsinki.fi/poxoPOXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.10277Tue, 15 May 2012 03:30:06 -0400 http://pre-s.protein.osaka-u.ac.jp/prebi/Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.10268Wed, 16 May 2012 19:50:03 -0400 http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.pyPREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.10306Wed, 16 May 2012 17:20:07 -0400 http://ps.cb.k.u-tokyo.ac.jp/PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.10278Sun, 13 May 2012 11:50:04 -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://cubic.bioc.columbia.edu/services/proftmb/PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.10263Mon, 14 May 2012 13:10:14 -0400 http://ProKware.mbc.nctu.edu.tw/ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.10249Wed, 16 May 2012 04:30:04 -0400 http://projects.villa-bosch.de/dbase/ps2/Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures10239Tue, 15 May 2012 19:40:07 -0400 http://protemot.csbb.ntu.edu.tw/The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.10307Thu, 17 May 2012 01:20:13 -0400 http://pseudoviewer.inha.ac.kr/PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.10135Tue, 15 May 2012 12:40:19 -0400 http://bioinformatics.albany.edu/~ptargetpTARGET predicts the subcellular localization of eukaryotic proteins based on the occurrence patterns of location-specific protein functional domains and the amino acid compositional differences in proteins from nine distinct subcellular locations.10219Wed, 16 May 2012 02:50:06 -0400 http://pupasuite.bioinfo.cipf.esPupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.9891Mon, 14 May 2012 22:40:06 -0400 http://bioinformatics.ramapo.edu/QGRS/index.phpQuadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.10254Thu, 17 May 2012 02:30:04 -0400 http://miracle.igib.res.in/quadfinder/QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.10280Thu, 17 May 2012 03:10:05 -0400 http://gibk26.bio.kyutech.ac.jp/jouhou/readout/Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.10292Wed, 16 May 2012 08:30:04 -0400 http://regrna.mbc.nctu.edu.tw/Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.10301Sun, 13 May 2012 10:10:11 -0400 http://140.121.196.30/remus.aspREinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.10233Tue, 15 May 2012 17:10:05 -0400 http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.10260Wed, 16 May 2012 00:50:09 -0400 http://bioinfo.csie.ncu.edu.tw/~rnamst/RNA Motif Search Tool (RNAMST) is a tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences.10247Mon, 14 May 2012 21:50:11 -0400 http://rosettadesign.med.unc.eduRosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.10228Wed, 16 May 2012 22:40:15 -0400 http://bioserv.rpbs.jussieu.fr/cgi-bin/SABBACStructural Alphabet based protein Backbone Builder from Alpha Carbon trace (SABBAC) is a tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.10289Wed, 16 May 2012 23:00:26 -0400 http://prosite.expasy.org/scanprosite/ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.9470Wed, 16 May 2012 21:50:16 -0400 http://www.ysbl.york.ac.uk/sgTarget/sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.10221Sat, 12 May 2012 18:40:10 -0400 http://sivirus.rnai.jp/siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.10237Thu, 17 May 2012 02:30:04 -0400 http://snpnavigator.net/SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.10297Wed, 16 May 2012 16:50:11 -0400 http://bioinfo.ebc.ee/snpmasker/SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.10079Thu, 17 May 2012 03:10:09 -0400 http://algorithm.cs.nthu.edu.tw/tools/SPRINGSorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results.10232Sat, 12 May 2012 22:40:08 -0400 http://distill.ucd.ie/spritz/Spritz is a tool for the prediction of disordered regions of proteins.10161Wed, 16 May 2012 12:40:06 -0400 http://sumosp.biocuckoo.org/SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).10236Tue, 15 May 2012 07:10:08 -0400 http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.10294Thu, 10 May 2012 09:30:04 -0400 http://oxytricha.princeton.edu/SWAKK/Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.10269Tue, 15 May 2012 10:20:08 -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://jbirc.jbic.or.jp/tact/Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.10291Tue, 08 May 2012 08:50:06 -0400 http://www.dddc.ac.cn/tarfisdock/Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.10080Wed, 16 May 2012 05:20:03 -0400 http://taverna.sourceforge.net/Taverna is a tool for creating and running bioinformatics workflows.9931Wed, 16 May 2012 07:30:07 -0400 http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.htmlTFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.9895Sun, 13 May 2012 23:30:07 -0400 http://tico.gobics.de/TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.10286Tue, 15 May 2012 06:00:07 -0400 http://bioinformatics.bc.edu/clotelab/transFoldtransFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.10235Tue, 15 May 2012 04:30:07 -0400 http://treedetv2.bioinfo.cnio.es/treedet/index.htmlTree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.10275Mon, 14 May 2012 04:30:09 -0400 http://www.bioinformatics.nl/tools/treedomTreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.10234Thu, 17 May 2012 02:00:03 -0400 http://www.cbs.dtu.dk/services/VirtualRibosome/The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results.10253Tue, 15 May 2012 14:20:34 -0400 https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jspVOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.10241Tue, 15 May 2012 07:40:06 -0400 http://wego.genomics.org.cn/cgi-bin/wego/index.plWeb Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.10193Wed, 16 May 2012 20:30:09 -0400 http://www.bahlerlab.info/YOGY/Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.10285Tue, 15 May 2012 20:20:04 -0400 http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.phpZinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.10224Wed, 16 May 2012 09:30:07 -0400