http://www.bioinformatics.ca/links_directory/journals/nar/2004http://www.bioinformatics.ca/links_directory/journals/nar/2004/feed en http://bibiserv.techfak.uni-bielefeld.de/agenda/AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.9218Wed, 16 May 2012 20:50:08 -0400 http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.plArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.9239Thu, 17 May 2012 02:10:08 -0400 http://www.snubi.org/software/ArrayXPath/ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.9240Thu, 10 May 2012 22:30:10 -0400 http://genome.ewha.ac.kr/ECgene/ASmodeler/Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.9248Wed, 16 May 2012 23:20:15 -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://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.9264Thu, 17 May 2012 01:30:17 -0400 http://bioinfo3d.cs.tau.ac.il/BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.9276Wed, 16 May 2012 23:10:07 -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://robotics.stanford.edu/~xsliu/BioProspector/Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.9289Sat, 12 May 2012 11:50:10 -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://www.bioinfo.no/tools/bompThe beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.9309Tue, 15 May 2012 05:00:05 -0400 http://iris.physics.iisc.ernet.in/bsdd/BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.9314Wed, 16 May 2012 04:00:07 -0400 http://bioinfo.lifl.fr/carnacServer which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.9323Mon, 14 May 2012 14:10:07 -0400 http://zlab.bu.edu/CARRIE-webServer which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.9302Sun, 13 May 2012 19:00:08 -0400 http://igs-server.cnrs-mrs.fr/Caspr/index.cgiCaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.9325Wed, 16 May 2012 15:10:10 -0400 http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgiCD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.9333Mon, 14 May 2012 10:10:07 -0400 http://bioinformatics.albany.edu/~cemc/A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.9335Sun, 13 May 2012 21:00:08 -0400 http://dialign.gobics.de/chaos-dialign-submissionThe CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.9339Tue, 15 May 2012 20:00:04 -0400 http://www.rostlab.org/services/CHOP/CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.9874Tue, 15 May 2012 17:30:05 -0400 http://cluspro.bu.edu/login.phpClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.9352Tue, 15 May 2012 12:00:05 -0400 http://asia.genesilico.pl/colorado3d/COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.9365Wed, 16 May 2012 01:30:04 -0400 http://compareprospector.stanford.edu/Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.9367Wed, 16 May 2012 23:30:04 -0400 http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.plThe Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.9916Thu, 17 May 2012 02:10:09 -0400 http://www.phylofoot.org/consite/Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.9373Wed, 16 May 2012 04:10:05 -0400 http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.9810Wed, 16 May 2012 11:00:13 -0400 http://creme.dcode.org/CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.9892Wed, 16 May 2012 02:10:06 -0400 http://www.caspur.it/CSTminer/CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.9390Wed, 16 May 2012 19:30:09 -0400 http://tlife.fudan.edu.cn/cvtreeComposition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.9392Wed, 16 May 2012 15:30:04 -0400 http://deqor.mpi-cbg.de/deqor_new/input.htmlTool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.9405Wed, 16 May 2012 09:50:18 -0400 http://bibiserv.techfak.uni-bielefeld.de/dialign/Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.9407Sat, 12 May 2012 02:50:08 -0400 http://dichroweb.cryst.bbk.ac.uk/html/home.shtmlA server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.9411Tue, 15 May 2012 03:40:07 -0400 http://bibiserv.techfak.uni-bielefeld.de/e2g/E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.9906Wed, 16 May 2012 15:50:17 -0400 http://ecrbrowser.dcode.org/The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.9903Mon, 14 May 2012 06:40:09 -0400 http://www.ncbi.nlm.nih.gov/sutils/e-pcrFind sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.10726Tue, 15 May 2012 19:00:06 -0400 http://igs-server.cnrs-mrs.fr/elnemo/start.htmlElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.9883Tue, 15 May 2012 09:50:05 -0400 http://tagc.univ-mrs.fr/erpin/ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.9822Wed, 16 May 2012 19:00:07 -0400 http://www.imtech.res.in/raghava/eslpred/ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.9842Mon, 07 May 2012 12:40:08 -0400 http://www.ebi.ac.uk/expressionprofiler/Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.9907Wed, 16 May 2012 19:40:06 -0400 http://fatcat.burnham.org/FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.9887Wed, 16 May 2012 20:40:05 -0400 http://foldminer.stanford.edu/FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.9866Sat, 12 May 2012 17:10:09 -0400 http://www.doe-mbi.ucla.edu/Services/GDAPThe Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.9834Wed, 16 May 2012 23:40:07 -0400 http://berry.engin.umich.edu/gene2oligo/Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).9826Wed, 16 May 2012 04:10:04 -0400 http://www.ncbi.nih.gov/projects/genotyping/formpage.cgiThe Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.9855Thu, 10 May 2012 14:30:06 -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://www.medinfopoli.polimi.it/GFINDer/Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.9905Wed, 16 May 2012 01:10:19 -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://www.imtech.res.in/raghava/gpcrpred/GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.9839Wed, 16 May 2012 00:50:06 -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://genopole.toulouse.inra.fr/bioinfo/Iccare/The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.9846Thu, 17 May 2012 02:30:14 -0400 http://cic.cs.wustl.edu/RNA/Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.9821Sat, 12 May 2012 07:30:05 -0400 http://imgt.cines.fr/The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.9847Tue, 15 May 2012 16:40:04 -0400 http://caps.ncbs.res.in/imot/iMOTserver.htmliMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.9890Tue, 15 May 2012 12:40:11 -0400 http://isofinder.sourceforge.net/IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.9904Wed, 09 May 2012 22:20:08 -0400 http://coco.protein.osaka-u.ac.jp/isotopica/Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.9850Thu, 17 May 2012 00:50:06 -0400 http://biryani.med.yale.edu/karma/cgi-bin/mysql/karma.plKARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.9898Sun, 13 May 2012 08:10:08 -0400 http://www.rostlab.org/services/LOCtarget/LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.9860Tue, 15 May 2012 23:40:09 -0400 http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.9880Wed, 16 May 2012 08:50:07 -0400 http://robotics.stanford.edu/~xsliu/MDscan/Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.9870Wed, 16 May 2012 23:00:06 -0400 http://basic.bioinfo.pl/Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.10718Mon, 14 May 2012 18:40:09 -0400 http://bioinformatics.albany.edu/~mitopred/MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.9836Mon, 14 May 2012 03:00:06 -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.9882Thu, 17 May 2012 02:30:15 -0400 http://monster.northwestern.edu/MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.9873Wed, 16 May 2012 20:20:05 -0400 http://biowulf.bu.edu/MotifViz/MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.9843Mon, 14 May 2012 22:10:09 -0400 http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.plMoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.9293Tue, 15 May 2012 05:40:05 -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, 14 May 2012 08:20:06 -0400 http://cubic.bioc.columbia.edu/services/nlprot/index.htmlNLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.9877Sun, 13 May 2012 14:50:07 -0400 http://www.nii.res.in/nrps-pks.htmlNRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.9841Wed, 16 May 2012 22:20:05 -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.pathblast.org/PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user.9814Wed, 16 May 2012 07:40:10 -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://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.9853Wed, 16 May 2012 05:50:15 -0400 http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.htmlPDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.9869Wed, 16 May 2012 17:40:06 -0400 http://www.imtech.res.in/bvs/pepbuild/PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format.10719Mon, 14 May 2012 13:10:05 -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://wishart.biology.ualberta.ca/PlasMapper/index.htmlWeb server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.9851Sun, 13 May 2012 08:40:09 -0400 http://ekhidna.biocenter.helsinki.fi/poxo/pobo/POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.9865Thu, 17 May 2012 00:20:12 -0400 http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.9838Wed, 16 May 2012 22:30:14 -0400 http://bioinformatics.biol.uoa.gr/PRED-TMBB/PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.9840Mon, 14 May 2012 18:10:08 -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.cdfd.org.in/predictregulon/PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.9827Wed, 16 May 2012 22:00:05 -0400 http://www.predisi.de/PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets.9837Wed, 16 May 2012 18:00:12 -0400 http://www.pathogenomics.ca/probelynxUsing current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.9915Mon, 14 May 2012 11:20:13 -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://proteomics.mcw.edu/promostProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.9876Wed, 16 May 2012 06:10:09 -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.9914Wed, 16 May 2012 23:10:18 -0400 http://csbl.bmb.uga.edu/protein_pipelineAn automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.9913Sat, 12 May 2012 22:40:12 -0400 http://proteindbs.rnet.missouri.edu/ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.9875Mon, 14 May 2012 10:50:08 -0400 http://www.cs.ualberta.ca/~bioinfo/PA/Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.9835Mon, 14 May 2012 22:30:10 -0400 http://pubcrawler.gen.tcd.ie/It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).9558Sun, 13 May 2012 23:20:10 -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://www.netasa.org/qgrid/index.htmlServer which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.9816Mon, 14 May 2012 12:50:08 -0400 http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.9831Tue, 15 May 2012 08:30:06 -0400 http://genes.mit.edu/burgelab/rescue-ese/Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.9852Sat, 12 May 2012 06:20:10 -0400 http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.htmlRNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.9554Tue, 15 May 2012 18:10:06 -0400 http://robetta.bakerlab.org/The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.9862Wed, 16 May 2012 19:10:08 -0400 http://rvista.dcode.org/Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.9864Wed, 16 May 2012 06:50:08 -0400 http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-SearchSA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.9868Sun, 13 May 2012 21:20:10 -0400 http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=mainThe SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.9825Wed, 16 May 2012 18:30:13 -0400 http://bioserv.rpbs.jussieu.fr/cgi-bin/SCitSCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure.9858Wed, 16 May 2012 18:40:11 -0400 http://proline.bic.nus.edu.sg/sdpmod/SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).9833Wed, 09 May 2012 23:20:06 -0400 http://bioinf.fbb.msu.ru/SDPpred/SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.9844Wed, 16 May 2012 08:10:05 -0400 http://zlab.bu.edu/SeqVISTA/Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.9475Mon, 14 May 2012 12:50:07 -0400 http://sfold.wadsworth.orgServer with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.9820Thu, 17 May 2012 00:40:05 -0400 http://design.RNAi.jp/Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.9818Tue, 15 May 2012 09:30:05 -0400 http://jura.wi.mit.edu/bioc/siRNAServer aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.9819Wed, 16 May 2012 23:30:07 -0400 http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.9861Tue, 15 May 2012 13:30:10 -0400 http://bioapps.rit.albany.edu/sledgeHMMER/SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.9867Tue, 15 May 2012 17:20:09 -0400 http://www.SNPbox.orgTool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.9824Tue, 15 May 2012 23:20:15 -0400 http://webclu.bio.wzw.tum.de/stride/STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.9848Tue, 15 May 2012 02:20:08 -0400 http://wishart.biology.ualberta.ca/SuperPose/SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.9894Tue, 15 May 2012 03:50:13 -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://www.ebi.ac.ukThe European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.11619Tue, 15 May 2012 11:20:05 -0400 http://www.cellbio.unige.ch/RNAi.htmlT7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.9817Sat, 12 May 2012 12:30:12 -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.9635Fri, 11 May 2012 19:10:06 -0400 http://wavis.img.cas.cz/The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.9808Wed, 16 May 2012 11:10:21 -0400 http://159.149.109.9/modtools/Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.9857Wed, 16 May 2012 14:00:09 -0400 http://interviewer.inha.ac.kr/WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.9815Tue, 15 May 2012 02:40:13 -0400 http://www.zbh.uni-hamburg.de/wurst/Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.9863Fri, 11 May 2012 22:00:07 -0400