http://bioinformatics.ca/links_directory/tag/molecular-sequence-datahttp://bioinformatics.ca/links_directory/tag/molecular-sequence-data/feed en http://compbio.cs.toronto.edu/ligalign/LigAlign: an automated system and structure visualization tool for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment. 13430Thu, 23 May 2013 09:00:53 -0400 http://www.compsysbio.org/elastin/ElastoDB is a repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties. 13426Tue, 21 May 2013 08:10:18 -0400 http://compbio.cs.utoronto.ca/varid/VARiD is a Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads. VARiD combines both types of data in a single framework which allows for accurate predictions.13398Thu, 23 May 2013 00:20:49 -0400 http://www.compsysbio.org/subseqer/A tool to find sequence motifs in low complexity protein sequences. SubSeqer uses the application of a unique graph based approach. 13383Wed, 22 May 2013 19:00:33 -0400 http://www.clotbase.bicnirrh.res.in/ClotBase is a curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases , mutation and links to external databases13234Wed, 22 May 2013 13:00:21 -0400 http://www.webscipio.orgScipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.13230Fri, 24 May 2013 08:20:18 -0400 http://www.imtech.res.in/raghava/alphapred/The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.12899Thu, 23 May 2013 05:30:31 -0400 http://www.imtech.res.in/raghava/betatpred2/The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.12897Fri, 24 May 2013 04:10:43 -0400 http://www.imtech.res.in/raghava/btevalThe aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.12895Fri, 24 May 2013 01:10:33 -0400 http://www.imtech.res.in/raghava/chpredictThe CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties. 12894Tue, 21 May 2013 13:10:22 -0400 http://www.biocomputing.it/pigs/Pigs is a web server for the automatic prediction and modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion. Its final output is a complete three-dimensional model of the target antibody that can be downloaded or displayed on-line.12833Fri, 24 May 2013 01:40:09 -0400 http://bioinformatics.vub.ac.be/software/software.htmlAlign-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.12646Tue, 21 May 2013 23:00:25 -0400 http://i.cs.hku.hk/~ckwong3/bwtsw/BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments (see BLAST Sensitivity), BWT-SW finds all local alignments.12636Thu, 23 May 2013 12:31:07 -0400 http://www.fml.tuebingen.mpg.de/raetsch/suppl/qpalmaQPalma is an alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.12632Sun, 19 May 2013 22:20:16 -0400 http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs (Site Identification from Short Sequence Reads), an algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. 12629Fri, 24 May 2013 11:20:23 -0400 http://vcake.sourceforge.net/VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data. 12621Tue, 21 May 2013 12:40:26 -0400 http://rulai.cshl.edu/rmap/RMAP is aimed to map accurately reads from the next-generation sequencing technology. RMAP can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There are no limitations on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.12614Fri, 17 May 2013 16:40:15 -0400 http://1001genomes.org/downloads/shore.htmlSHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. 12612Wed, 22 May 2013 08:20:29 -0400 http://www-bimas.cit.nih.gov/molbio/hla_bind/Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.12392Tue, 21 May 2013 17:50:16 -0400 http://www.syfpeithi.de/SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. The database can be used to predict the immunogenicity of given peptide sequences.12391Mon, 20 May 2013 14:00:16 -0400 http://bioinfo.townsend.yale.edu/The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.12246Thu, 23 May 2013 17:30:34 -0400 http://www.pseudomonas.comThe Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.11924Fri, 17 May 2013 15:30:14 -0400 http://db.psort.orgPSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset). 11819Thu, 23 May 2013 08:10:26 -0400 http://www.ebi.ac.uk/ipd/The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines.11751Thu, 23 May 2013 07:40:48 -0400 http://pga.mgh.harvard.edu/primerbank/PrimerBank is a public resource for the retrieval of human and mouse primer pairs for gene expression analysis by PCR and Quantitative PCR (QPCR). Information on these primers such as T(m), location on the transcript and amplicon size is also included. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. There are several ways to search for primers for the gene(s) of interest, such as by: GenBank accession number, NCBI protein accession number, NCBI gene ID, PrimerBank ID, NCBI gene symbol or gene description (keyword). Primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site.11741Fri, 24 May 2013 03:00:34 -0400 http://www.seltarbase.orgThe Selective Targets database is a curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite instability (MSI) -H tumor entities indicating statistically deviant mutation frequencies predict genes that are shown or highly suspected to be involved in MSI tumorigenesis. Many useful tools for further analyzing genomic DNA, derived wild-type and mutated cDNAs and peptides are integrated. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is also included.11725Fri, 24 May 2013 09:50:32 -0400 http://www.yeastgenome.org/The Saccharomyces Genome Database (SGD) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Phenotypes and genetic interaction data are also annotated and displayed in SGD.11685Fri, 24 May 2013 09:40:35 -0400 http://pathema.jcvi.orgPathema is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses.11681Mon, 20 May 2013 22:10:27 -0400 http://www.genome.ad.jp/keggThe KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.11672Sun, 19 May 2013 21:50:35 -0400 http://www.ebi.ac.uk/pdbe/The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. The database infrastructure is based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serves as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.11664Fri, 24 May 2013 12:50:27 -0400 http://www.imgt.org/3Dstructure-DB/IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system for immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin and MHC superfamilies (IgSF and MhcSF, respectively) and found in complexes with IG, TR or MHC. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY concepts and axioms. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. In its Web version, the IMGT/DomainGapAlign tool analyses amino acid sequences, per domain.11663Fri, 24 May 2013 07:30:08 -0400 http://rna.urmc.rochester.edu/NNDBThe Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes.11659Thu, 23 May 2013 08:20:32 -0400 http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?searchThe ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs.11658Thu, 23 May 2013 12:50:24 -0400 http://merops.sanger.ac.uk/The MEROPS database is a collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database can distinguish one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact.11651Wed, 22 May 2013 09:00:29 -0400 http://pfam.sanger.ac.uk/Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.11649Thu, 23 May 2013 14:20:40 -0400 http://prosite.expasy.org/PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. PROSITE is used for the annotation of domain features of UniProtKB/Swiss-Prot entries. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases their discriminatory power by providing additional information about functionally and/or structurally critical amino acids. 11643Fri, 24 May 2013 15:50:36 -0400 http://recode.ucc.ieRecode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon redefinition. Recode-2 provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements.11628Mon, 20 May 2013 04:50:15 -0400 http://pseudomonas.com/This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information.11442Fri, 24 May 2013 04:30:42 -0400 http://ndbserver.rutgers.edu/NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids.11431Wed, 22 May 2013 03:20:24 -0400 http://db.psort.org/PSORTdb is a database of proteins of experimentally known (ePSORTdb) and computationally predicted (cPSORTdb) subcellular localization.11432Fri, 24 May 2013 09:20:21 -0400 http://www.genome.ad.jp/kegg/Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.11391Thu, 23 May 2013 14:40:20 -0400 http://www.vessels.bwh.harvard.edu/This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.11301Fri, 24 May 2013 00:50:43 -0400 http://bioserv.rpbs.jussieu.fr/Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).11312Thu, 23 May 2013 13:40:37 -0400 http://salilab.org/our_resources.shtmlThis page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).11316Thu, 23 May 2013 21:40:29 -0400 http://genomebiology.com/series/drosophilaA series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.11237Thu, 23 May 2013 13:20:21 -0400 http://www.fruitfly.org/Good entrez to fly genome resources.11230Thu, 23 May 2013 19:50:17 -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.10726Wed, 22 May 2013 22:50:40 -0400 https://mutalyzer.nl/Mutalyzer was primarily developed to check the description of sequence variants identified in a gene during genetic testing according to the rules of the standard human sequence variant nomenclature of the Human Genome Variation Society. The Mutalyzer 2 parser is based on a formalized description of the nomenclature in Extended Backus-Naur Form. Mutalyzer applies the nomenclature rules and corrects variant descriptions accordingly.10620Thu, 23 May 2013 18:40:21 -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.10615Thu, 23 May 2013 05:50:07 -0400 http://prep.unl.edu/The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.10567Mon, 20 May 2013 09:30:12 -0400 http://www.cmbi.ru.nl/phylopatPhyloPat is a webserver which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. The output can be saved in HTML, Excel or plain text format for further analysis. Output is linked to the FatiGO web interface creating easy access to functional information.10505Fri, 24 May 2013 07:50:31 -0400 http://topmatch.services.came.sbg.ac.at/TopMatch is a computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications.10507Sat, 18 May 2013 07:40:21 -0400 http://dna.cs.byu.edu/treesaap/The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests.10511Mon, 20 May 2013 05:40:18 -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.10422Thu, 23 May 2013 15:10:43 -0400 http://cbm.bio.uniroma2.it/SH3-Hunter/SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.10418Fri, 24 May 2013 18:10:28 -0400 http://lorentz.immstr.pasteur.fr/joel/index.phpMinActionPath calculates the most-probable trajectory between two known structural states of a protein.10415Wed, 22 May 2013 07:00:11 -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.10413Thu, 23 May 2013 19:20:21 -0400 http://bioinformatics.bc.edu/clotelab/RNAbor/RNAbor is a server for computing structural neighbors of a RNA secondary structure.10412Thu, 23 May 2013 09:00:40 -0400 http://bindr.gdcb.iastate.edu/RNABindR/RNABindR is a server for analyzing and predicting RNA binding sites in proteins.10405Fri, 24 May 2013 12:00:20 -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).10390Tue, 21 May 2013 14:40:33 -0400 http://biominer.bime.ntu.edu.tw/ipda/iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.10392Thu, 23 May 2013 05:30:20 -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, 24 May 2013 07:10:26 -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.10401Tue, 21 May 2013 16:00:22 -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://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.10382Thu, 23 May 2013 03:00:24 -0400 http://selecton.tau.ac.il/Selecton is a server for the identification of site-specific positive selection and purifying selection.10378Wed, 22 May 2013 18:40:30 -0400 http://indelscan.genomics.sinica.edu.tw/IndelScan/INDELSCAN is a tool for genome-wide identification of indels.10366Fri, 24 May 2013 09:10:17 -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://www.bioinf.seu.edu.cn/miRNA/miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.10375Thu, 23 May 2013 10:30:35 -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.10376Fri, 24 May 2013 06:10:17 -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.10363Fri, 24 May 2013 15:10:17 -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://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.10335Fri, 24 May 2013 15:40:12 -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://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://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.10331Wed, 22 May 2013 10:50:33 -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.10330Fri, 24 May 2013 02:10:52 -0400 http://www.umsl.edu/services/kellogg/primaclade.htmlPrimaclade accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers that will bind across the alignment.10325Wed, 22 May 2013 10:30:24 -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.10291Fri, 24 May 2013 14:00:12 -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.10290Thu, 23 May 2013 23:40:40 -0400 http://www.dsimb.inserm.fr/dsimb_tools/peeling3/Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.10276Tue, 21 May 2013 19:00:17 -0400 http://treedetv2.bioinfo.cnio.es/treedet/index.htmlTree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.10275Tue, 21 May 2013 06:10:16 -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.10267Tue, 21 May 2013 00:30:21 -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.10224Mon, 20 May 2013 20:30:09 -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.10228Fri, 24 May 2013 12:10:13 -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.10233Wed, 22 May 2013 18:40:19 -0400 http://ndbserver.rutgers.edu/services/The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.10220Wed, 22 May 2013 23:30:32 -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.10219Fri, 24 May 2013 17:50:24 -0400 http://darwin.uvigo.es/software/prottest_server.html?ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.10210Mon, 20 May 2013 19:00:22 -0400 http://www.biw.kuleuven.be/logt/PHIRE.htmPhage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes.10199Thu, 23 May 2013 13:20:08 -0400 http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=92A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.10187Thu, 23 May 2013 03:30:44 -0400 http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.10195Tue, 21 May 2013 18:40:28 -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.10194Fri, 24 May 2013 16:50:21 -0400 http://icb.med.cornell.edu/crt/RbDe/index.xmlResidue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.10183Wed, 22 May 2013 11:00:26 -0400 http://bips.u-strasbg.fr/PipeAlign/PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.10177Fri, 24 May 2013 15:00:34 -0400 http://www.geno2pheno.org/cgi-bin/geno2pheno.plGeno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.10182Thu, 23 May 2013 08:30:26 -0400 http://bio.math.berkeley.edu/mavid/download/MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.10166Fri, 24 May 2013 14:50:10 -0400 http://distill.ucd.ie/spritz/Spritz is a tool for the prediction of disordered regions of proteins.10161Sat, 18 May 2013 21:30:29 -0400 http://pseudoviewer.inha.ac.kr/PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.10135Tue, 21 May 2013 04:40:12 -0400 http://cbm.bio.uniroma2.it/ispot/iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.10130Tue, 21 May 2013 09:00:16 -0400 http://www.daimi.au.dk/~compbio/pfoldThe Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.10137Thu, 23 May 2013 21:50:15 -0400 http://mendel.imp.ac.at/The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.10118Thu, 09 May 2013 19:50:13 -0400 http://www.nematodes.org/nembase4/NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design. 10082Fri, 24 May 2013 15:00:19 -0400 http://luna.bioc.columbia.edu/SMS/STINGm/STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.10042Fri, 24 May 2013 05:20:42 -0400 http://www.mlst.net/MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.10016Thu, 23 May 2013 18:40:26 -0400 http://www.cbs.dtu.dk/services/OligoWiz2/OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.10017Fri, 24 May 2013 15:40:23 -0400 http://ibivu.cs.vu.nl/programs/pralinewww/Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.9976Thu, 23 May 2013 05:20:24 -0400 http://gpcr.biocomp.unibo.it/biodec/TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.9971Fri, 24 May 2013 03:40:26 -0400 http://smart.embl-heidelberg.de/SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins.9966Wed, 22 May 2013 04:40:14 -0400 http://lowelab.ucsc.edu/snoGPS/snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence9947Mon, 20 May 2013 17:20:08 -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.9895Thu, 23 May 2013 22:10:21 -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.9887Sun, 19 May 2013 12:50:16 -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, 20 May 2013 14:20:20 -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.9831Thu, 23 May 2013 23:30:40 -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.9817Wed, 22 May 2013 05:30:15 -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.9818Fri, 24 May 2013 16:10:30 -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.9820Fri, 24 May 2013 14:50:20 -0400 http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.plJASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.9802Tue, 21 May 2013 17:00:28 -0400 http://www.rnasoft.ca/Software for RNA/DNA secondary structure prediction and design9760Fri, 24 May 2013 17:50:19 -0400 http://elm.eu.org/Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.9733Wed, 22 May 2013 00:50:30 -0400 http://sonnhammer.sbc.su.se/Dotter.htmlDotter is a dot-matrix program with interactive greyscale rendering for genomic DNA and protein sequence analysis.9707Fri, 24 May 2013 05:20:09 -0400 http://lagan.stanford.edu/lagan_web/index.shtmlThe LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment program), Multi-LAGAN , and Shuffle-LAGAN (both variations of LAGAN).9705Fri, 24 May 2013 14:30:21 -0400 http://www.cbs.dtu.dk/services/NetGene2/The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.9676Fri, 24 May 2013 16:10:13 -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.9642Thu, 23 May 2013 23:40:34 -0400 http://us.expasy.org/tools/peptide-mass.htmlCleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.9612Thu, 23 May 2013 20:40:25 -0400 http://www.ebi.ac.uk/Tools/saps/Calculations include compositional analysis, charge distribution, identification of highly hydrophobic (transmembrane) segments, sequence repeats, and more.9611Mon, 20 May 2013 17:40:22 -0400 http://www.cbs.dtu.dk/services/NetOGlyc/Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins.9609Sat, 18 May 2013 13:20:55 -0400 http://helix-web.stanford.edu/sstructview/home.htmlRNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.9593Sun, 19 May 2013 20:40:27 -0400 http://fasta.bioch.virginia.edu/Sequence retrieval and comparison tools.9600Wed, 22 May 2013 16:50:41 -0400 http://staden.sourceforge.net/UNIX-based tools for sequence assembly, mutation detection and sequence analysis; free for non-commercial use. Note that Staden development and support have ceased due to lack of funding, despite widespread use.9586Sun, 19 May 2013 13:50:08 -0400 http://metameme.sdsc.edu/Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.9560Fri, 24 May 2013 11:20:35 -0400 http://www.genome.ad.jp/Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast, Motif, Clustal W)9547Sat, 18 May 2013 22:20:18 -0400 http://www.sagenet.org/Serial Analysis of Gene Expression; simultaneous expression and map information.9557Fri, 17 May 2013 23:30:20 -0400 http://compbio.dfci.harvard.edu/tgi/An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.9534Sun, 19 May 2013 20:10:14 -0400 http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.htmlProtein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.9485Fri, 24 May 2013 00:00:51 -0400 http://genes.mit.edu/GENSCAN.htmlIdentification of complete gene structures in genomic DNA.9492Tue, 21 May 2013 21:40:24 -0400 http://www.expasy.ch/swissmod/SWISS-MODEL.htmlAutomated protein modelling server.9486Tue, 21 May 2013 18:40:14 -0400 http://www.psort.org/PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.9473Mon, 20 May 2013 02:20:27 -0400 http://bmerc-www.bu.edu/psa/request.htmPrediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.9479Fri, 24 May 2013 03:30:49 -0400 http://primer3.sourceforge.net/Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.9454Thu, 23 May 2013 05:30:40 -0400 http://www.fugu-sg.org/Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.9449Thu, 23 May 2013 23:50:45 -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://disulfind.dsi.unifi.it/DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.9419Fri, 24 May 2013 02:50:40 -0400 http://mfold.rna.albany.edu/?q=DINAMeltDINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.9413Wed, 22 May 2013 16:30:25 -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.9407Fri, 24 May 2013 08:40:13 -0400 http://datf.cbi.pku.edu.cnThe Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.9398Fri, 24 May 2013 11:40:14 -0400 http://fasta.bioch.virginia.edu/crp/Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.9387Thu, 23 May 2013 06:10:42 -0400 http://www.cpndb.ca/cpnDB/home.phpcpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.9383Thu, 23 May 2013 22:10:56 -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.9381Thu, 23 May 2013 17:00:16 -0400 http://cl.sdsc.edu/ce.htmlCalculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.9366Fri, 24 May 2013 02:30:14 -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.9356Wed, 22 May 2013 20:20:11 -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.9335Fri, 24 May 2013 13:30:16 -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).9324Thu, 23 May 2013 18:10:35 -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, 22 May 2013 23:40:36 -0400 http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.9270Wed, 22 May 2013 10:30:17 -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.9265Wed, 22 May 2013 19:00:10 -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.9254Wed, 22 May 2013 19:40:13 -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.9248Tue, 21 May 2013 10:10:14 -0400 http://genome.ewha.ac.kr/ASePCR/ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.9247Fri, 24 May 2013 15:20:30 -0400 http://motif.stanford.edu/distributions/3motif/3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.9212Sun, 19 May 2013 08:30:17 -0400 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.9207Wed, 22 May 2013 01:20:22 -0400