http://bioinformatics.ca/links_directory/tag/ratshttp://bioinformatics.ca/links_directory/tag/rats/feed en http://download.baderlab.org/BINDTranslation/Biomolecular Interaction Network Database (BIND): a database of curated biomolecular interactions.13415Tue, 21 May 2013 07:50:20 -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.13230Mon, 20 May 2013 10:50:15 -0400 http://www.esat.kuleuven.be/endeavourENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.12956Mon, 20 May 2013 08:40:14 -0400 http://www.polygenicpathways.co.ukThe datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helicobacter pylori and the HIV-1/AIDS virus.12756Mon, 20 May 2013 18:40:29 -0400 http://pilgrm.princeton.eduThe Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries.12187Wed, 22 May 2013 00:00:40 -0400 http://www.btool.org/ADGO2ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.12158Tue, 21 May 2013 10:50:23 -0400 http://www.BioProfiling.de/gene_list.BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.12152Mon, 20 May 2013 15:40:22 -0400 http://mirvestigator.systemsbiology.netmiRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).12123Sun, 19 May 2013 09:00:15 -0400 http://www.esat.kuleuven.be/pinta/PINTA is a web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA is available for 5 species (human, mouse, rat, worm and yeast).12115Sat, 18 May 2013 11:00:42 -0400 http://www.t1dbase.orgT1DBase is a database for type 1 diabetes (T1D). It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci, incorporating genetic overlap with other related diseases.11918Sun, 19 May 2013 12:50:24 -0400 http://coxpresdb.jpCOXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.11795Mon, 20 May 2013 14:30:14 -0400 http://www.lm.lncc.brThe Laminin(LM)-database is a database focusing on the non-collagenous extracellular matrix protein family, the LMs. The homepage is subdivided into LMs, receptors, extracellular binding and other related proteins. Each tab opens into a given LM or LM-related molecule, where the reader finds a series of further tabs for 'protein', 'gene structure', 'gene expression' and 'tissue distribution' and 'therapy'. Data are separated as a function of species, comprising Homo sapiens, Mus musculus and Rattus novergicus.11791Tue, 21 May 2013 12:50:49 -0400 http://kpv.kazusa.or.jp/kpv4/KaPPA-View4 is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version. Gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.11780Mon, 20 May 2013 23:00:20 -0400 http://mips.gsf.de/genre/proj/corumCORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 different genes, representing approximately 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. A 'Phylogenetic Conservation' analysis tool allows one to predict the occurrence of protein complexes in different phylogenetic groups.11697Sun, 19 May 2013 19:20:27 -0400 http://inparanoid.sbc.su.se/cgi-bin/index.cgiThe InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.11647Mon, 20 May 2013 23:10:24 -0400 http://eggnog.embl.de/version_2/eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).s (built from 2,590,259 proteins) and provides a broad functional description for at least 1,966,709 (88%) of them.11646Tue, 14 May 2013 05:10:30 -0400 http://ercsb.ewha.ac.kr/fusiongeneChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.11630Sun, 19 May 2013 15:30:52 -0400 http://rgd.mcw.edu/The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis.11418Mon, 20 May 2013 03:10:22 -0400 http://source.stanford.eduStanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.11384Tue, 21 May 2013 15:10:24 -0400 http://www.ncbi.nlm.nih.gov/RefSeq/Downloadable human DNA reference sequence as well as other reference genome sequences.11397Mon, 20 May 2013 15:40:06 -0400 http://phospho.elm.eu.org/Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data formerly found in PhosphoBase.11368Tue, 21 May 2013 22:30:21 -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).11312Sat, 18 May 2013 22:30:31 -0400 http://wavi.bioinfo.cnio.eswaviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.10690Tue, 21 May 2013 11:40:27 -0400 http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.10593Mon, 20 May 2013 09:50:28 -0400 http://www.mirz.unibas.chMirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.10582Tue, 21 May 2013 12:50:59 -0400 http://gopubmed.biotec.tu-dresden.de/gogeneGoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.10541Wed, 22 May 2013 03:10:24 -0400 http://www.ncrna.org/idiographica/Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface.10520Mon, 20 May 2013 14:10:31 -0400 http://mips.gsf.de/genre/proj/orest/index.htmlOnline Resource for EST (OREST) analysis is a EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. Functional annotation of the dataset is also included via either FunCat or GO annotation.10496Tue, 21 May 2013 04:50:18 -0400 http://hub.iis.sinica.edu.tw/HubbaHub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.10455Sun, 19 May 2013 13:20:33 -0400 http://bioware.ucd.ie/~slimdisc/SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.10413Sun, 19 May 2013 02:10:15 -0400 http://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.10301Mon, 20 May 2013 18:10:15 -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://bio.math.berkeley.edu/mavid/download/MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.10166Tue, 21 May 2013 13:20:27 -0400 http://alggen.lsi.upc.es/ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.10122Sun, 19 May 2013 22:50:16 -0400 http://synor.dcode.org/SynoR searches vertebrate genomes for synonymous regulatory elements.10064Mon, 20 May 2013 08:30:07 -0400 http://csbl.bmb.uga.edu/~ffzhou/gps_web/Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.9949Mon, 20 May 2013 08:30:10 -0400 http://compbio.dfci.harvard.edu/tgi/cgi-bin/magic/r1.plTool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) databases.9942Tue, 21 May 2013 13:50:18 -0400 http://mulan.dcode.org/Mulan is a multiple sequence alignment tool. It employs novel algorithms such as TBA and multiTF to respectively perform alignments and discover transcription factor binding sites. Results can be viewed as dot-plots of individual sequence alignments, or dynamically browsed with the ability to zoom in from sequence conservation profiles down to the level of the individual characters of the sequence alignment.9933Mon, 20 May 2013 21:50:25 -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.9903Sun, 19 May 2013 07:30:26 -0400 http://promoterplot.fmi.ch/PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool.9888Sun, 19 May 2013 14:10:21 -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, 21 May 2013 22:00:25 -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.9854Tue, 21 May 2013 22:00:17 -0400 http://www.genmapp.org/GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.9775Tue, 21 May 2013 03:40:25 -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).9705Tue, 21 May 2013 18:10:18 -0400 http://www.ebi.ac.uk/IPI/IPI provides a top level view of the human, mouse and rat proteome data found in Swiss-Prot, TrEMBL, RefSeq and Ensembl.9693Sat, 18 May 2013 23:40:18 -0400 http://www.bcgsc.ca/platform/bioinfo/software/iceViewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.9533Tue, 21 May 2013 00:50:43 -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.9413Tue, 21 May 2013 00:30:23 -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.9407Wed, 22 May 2013 02:40:45 -0400 http://www.copub.orgCoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.9377Sat, 18 May 2013 22:40:17 -0400 http://conreal.niob.knaw.nl/CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.9371Mon, 20 May 2013 12:20:25 -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.9339Sat, 18 May 2013 08:30:33 -0400 http://www.brenda-enzymes.org/Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.9313Tue, 21 May 2013 23:00:26 -0400 http://www.fatigo.org/FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.9307Mon, 20 May 2013 08:10:16 -0400 http://bioinfo.lifl.fr/TFMTFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.9296Tue, 21 May 2013 22:40:21 -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.9247Mon, 20 May 2013 08:20:15 -0400