http://bioinformatics.ca/links_directory/category/model-organisms/databasesThis section contains databases of model organism genomes, vertebrate/non-vertebrate/plant/organelle genomes, and taxonomy/identification.http://bioinformatics.ca/links_directory/category/model-organisms/databases/feed en http://www.agbase.msstate.edu/AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.11803Fri, 17 May 2013 10:20:31 -0400 http://arabidopsis.med.ohio-state.edu/The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.11835Wed, 15 May 2013 23:10:40 -0400 http://ahd.cbi.pku.edu.cn/Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.11859Mon, 20 May 2013 09:10:21 -0400 http://AmoebaDB.orgAmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.11887Mon, 20 May 2013 07:10:13 -0400 http://www.bioguo.org/AnimalTFDB/Comprehensive TF database; identified and classified all the genome-wide TFs in 50 sequenced animal genomes. Also collects transcription co-factors and chromatin remodeling factors of those genomes, which are also essential in the gene transcription regulation. 13365Sun, 19 May 2013 22:00:21 -0400 http://www.arachnoserver.orgArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.11882Fri, 17 May 2013 00:10:22 -0400 http://www.aspgd.org/An organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. 13510Fri, 17 May 2013 05:30:19 -0400 http://www.aspergillusgenome.org/The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.11683Thu, 16 May 2013 02:40:33 -0400 http://www.megabionet.org/atpid/The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.11876Mon, 20 May 2013 11:40:06 -0400 http://bacmap.wishartlab.com/An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. 13503Sat, 18 May 2013 22:00:13 -0400 http://beetlebase.org/BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. Genome information is visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools.11686Sun, 19 May 2013 15:20:12 -0400 http://bgee.unil.ch/Bgee is a dataBase for Gene Expression Evolution. It allows one to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.12238Sat, 18 May 2013 06:40:13 -0400 http://central.biomart.org/BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-database searches that might otherwise require several complicated steps.13435Sun, 19 May 2013 22:00:34 -0400 http://BovineGenome.orgThe Bovine Genome Database (BGD) includes mechanisms too improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. 11760Sat, 18 May 2013 19:00:11 -0400 http://bugs.sgul.ac.uk/bugsbase/A relational database containing microbial gene expression and comparative genomic hybridisation experimental data. The data is mostly derived from whole genome microarrays designed by the BµG@S group, however data from other microarrays is included and the database is being modified to support RNA-Seq analysis. Public access is available for datasets that have been published and login credentials can be obtained for data submission. 13504Mon, 20 May 2013 10:10:14 -0400 http://www.cadre-genomes.org.uk/index.htmlCentral Aspergillus Data REpository: public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available. 13511Tue, 14 May 2013 12:50:18 -0400 http://camera.calit2.net/The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. Users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC). CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.11868Sun, 19 May 2013 02:10:17 -0400 http://www.candidagenome.org/The Candida Genome Database provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.11684Thu, 16 May 2013 07:40:44 -0400 http://docs.bioinfo.cipf.es/projects/cellbaseCellBase is a relational database that contains relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. Integrated are the most relevant repositories such as Ensembl, Uniprot, Omim, COSMIC, IntAct, HapMap, Reactome, and others.13827Mon, 20 May 2013 12:00:15 -0400 http://www.fusariumdb.org/The Cyber infrastructure for Fusarium (CiF) consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. The FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them using multiple tools without requiring repeated copying-and-pasting of sequences.11794Thu, 16 May 2013 02:50:36 -0400 http://cipro.ibio.jp/2.5The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website. 11822Wed, 15 May 2013 15:50:08 -0400 http://combrex.bu.eduCOMBREX is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.11773Sun, 19 May 2013 12:11:48 -0400 http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgiThe Comprehensive Microbial Resource provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available.11670Fri, 10 May 2013 22:10:32 -0400 http://www.conoserver.org/Database specializing in the sequences and structures of conopeptides, toxins expressed by marine cone snails. 13463Mon, 13 May 2013 04:50:11 -0400 http://cpdb.molgen.mpg.deConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.11808Thu, 16 May 2013 21:30:26 -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://genome.kazusa.or.jp/cyanobaseCyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information.11676Sun, 19 May 2013 13:10:46 -0400 http://www.dictybase.orgdictyBase, the model organism database for Dictyostelium, provides well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a 'reference genome' in the Amoebozoa clade. New features include ortholog display and the complete integration of the Dicty Stock Center with dictyBase.11790Sun, 19 May 2013 01:50:17 -0400 http://dnatraffic.ibb.waw.pl/Database dedicated to comprehensive and rich annotations of genome dynamics during cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study.13583Sun, 19 May 2013 23:10:43 -0400 http://droidb.org/DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.11877Sun, 19 May 2013 05:50:22 -0400 http://drygin.ccbr.utoronto.ca/DRYGIN (Data Repository of Yeast Genetic Interactions)-a web database system that provides a central platform for yeast genetic network analysis and visualization. DRYGIN searches SGA interactions and integrates other data sources, in order to associate the genetic interactions with pathway information, protein complexes, other binary genetic and physical interactions, and Gene Ontology functional annotation.11698Wed, 15 May 2013 08:30:28 -0400 http://EcoCyc.orgEcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. New features include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity.11777Sun, 19 May 2013 22:40:15 -0400 http://www.emouseatlas.org/emage/EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.11728Tue, 14 May 2013 21:10:17 -0400 http://www.emmanet.orgThe European Mouse Mutant Archive (EMMA) is an infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl.11709Wed, 15 May 2013 18:30:33 -0400 http://www.ensembl.orgThe Ensembl project provides high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish.11864Mon, 20 May 2013 02:40:19 -0400 http://www.ensemblgenomes.orgEnsembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.11708Thu, 16 May 2013 16:20:17 -0400 http://EuPathDB.orgEuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. EuPathDB currently supports more than 80 searches. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.11682Sun, 19 May 2013 06:30:21 -0400 http://www.europhenome.org/The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.11710Sun, 19 May 2013 16:50:21 -0400 http://mips.gsf.de/genre/proj/FGDB/The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database for Fusarium graminearum. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets.11850Mon, 20 May 2013 03:30:07 -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.12246Sun, 12 May 2013 06:10:21 -0400 http://pgfe.umassmed.edu/TFDBS/FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.11782Mon, 20 May 2013 08:10:18 -0400 http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.htmlFlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.11687Mon, 20 May 2013 14:30:13 -0400 http://fullmal.hgc.jp/Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources were interconnected with our original database functionalities. By providing the largest unique full-length cDNA and dynamic transcriptome data, Full-Parasites is useful for understanding host-parasite interactions.11852Mon, 20 May 2013 00:00:18 -0400 http://www.gabi-kat.de/GABI-Kat: sequence-indexed collections of T-DNA insertion lines of Arabidopsis thaliana.13579Sun, 19 May 2013 09:30:26 -0400 http://gemina.igs.umaryland.eduThe Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.11736Sun, 19 May 2013 03:30:20 -0400 http://www.informatics.jax.orgThe Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants. GXD places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases. Web-based query forms support simple or complex searches. All data are annotated and reviewed by GXD curators.11833Sun, 12 May 2013 01:00:18 -0400 http://rnai2.dkfz.deThe GenomeRNAi database contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome. GenomeRNAi also facilitates the integration with other genomic data sets and contains expression profiling (RNA-Seq) data for several cell lines commonly used in RNAi experiments.11688Mon, 20 May 2013 11:50:22 -0400 http://www.geneontology.org/The Gene Ontology (GO) Consortium (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.11668Mon, 20 May 2013 14:50:22 -0400 http://www.genomesonline.org/The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. GOLD is in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.11671Sun, 19 May 2013 10:30:14 -0400 http://www.gramene.orgThe Gramene database has become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database.11799Mon, 20 May 2013 06:40:07 -0400 http://southgreen.cirad.fr/GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided.11933Sun, 19 May 2013 18:00:17 -0400 http://HymenopteraGenome.orgThe Hymenoptera Genome Database (HGD) is a comprehensive model organism database for insect species of the order Hymenoptera. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches.11821Sun, 19 May 2013 22:00:06 -0400 http://ophid.utoronto.ca/ophidv2.201/To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.13416Sun, 19 May 2013 22:50:38 -0400 http://db-mml.sjtu.edu.cn/ICEberg/Web-based resource for integrative and conjugative elements (ICEs) found in bacteria.13506Sun, 19 May 2013 23:10:45 -0400 http://igrcid.ibms.sinica.edu.twIGRhCellID is designed to integrate eight cell identification methods including seven methods (STR profile, gender, immunotypes, karyotype, isoenzyme profile, TP53 mutation and mutations of cancer genes) available in various public databases and our method of profiling genome alterations of human cell lines. Users can search for human cell lines with deleted gene to serve as indigenous knock-out cell model, with amplified gene to be the cell models for testing therapeutic efficacy and with overlapped aberrant chromosomal loci for revealing common cancer genes.11856Fri, 17 May 2013 11:10:14 -0400 http://www.knockoutmouse.orgThe International Knockout Mouse Consortium (IKMC) database and web portal serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority. The IKMC database provides data to, and features extensive interconnections with, other community databases.11925Thu, 16 May 2013 07:10:26 -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.9449Mon, 20 May 2013 01:50:41 -0400 http://img.jgi.doe.gov/The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context.11677Fri, 17 May 2013 06:30:15 -0400 http://isobase.csail.mit.edu/IsoBase is a database identifying functionally related proteins across five major eukaryotic model organisms: yeast, fly, worm, mouse, and human. Clusters were computed using the IsoRankN algorithm, which uses spectral methods, to combine sequence and PPI data to produce clusters of functionally related proteins. IsoBase may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword.11755Thu, 16 May 2013 14:00:14 -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://plantgrn.noble.org/LegumeIP/LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes.13581Wed, 15 May 2013 05:50:06 -0400 http://comparative-legumes.org/The Legume Information System enables productive applied and basic research in the legumes by relating data from multiple crop and model species, and by helping researchers traverse among various data types.12652Sun, 19 May 2013 09:50:28 -0400 http://www.eplantsenescence.org/This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf senescence or morphological phenotypes. Users can browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases. 11786Sun, 19 May 2013 13:30:35 -0400 http://genome.ufl.edu/mapperdbThe MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.13366Sun, 19 May 2013 03:40:24 -0400 http://www.Megx.netMegx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. With the Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. 11678Mon, 20 May 2013 11:10:16 -0400 http://www.MicrobesOnline.orgMicrobesOnline portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources.11679Mon, 20 May 2013 05:40:14 -0400 http://mbgd.genome.ad.jp/The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create ortholog groups using a specified subgroup of organisms. Advanced functionalities include: (i) enhanced assignment of functional annotation, including external database links to each orthologous group, (ii) interface for choosing a set of genomes to compare based on phenotypic properties, (iii) the addition of more eukaryotic microbial genomes (fungi and protists) and some higher eukaryotes as references and (iv) enhancement of the MyMBGD mode, which allows users to add their own genomes to MBGD and now accepts raw genomic sequences without any annotation (in such a case, it runs a gene-finding procedure before identifying the orthologs).11673Mon, 20 May 2013 00:40:20 -0400 http://lemur.amu.edu.pl/share/php/mirnest/home.phpmiRNEST: a comprehensive database of animal, plant and virus microRNAs. 13372Fri, 17 May 2013 19:50:36 -0400 http://genomics.ornl.gov/mist/The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface.11680Mon, 20 May 2013 07:10:18 -0400 http://mi.caspur.it/mitozoa/A database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa.13573Wed, 15 May 2013 05:50:15 -0400 http://mmmdb.iab.keio.ac.jp/Mouse Multiple Tissue Metabolome Database: metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. 13530Thu, 16 May 2013 07:40:50 -0400 http://www.informatics.jax.org/The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).11841Mon, 20 May 2013 09:30:16 -0400 http://www.mousebook.org/The MouseBook databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information. MouseBook can be searched either using an intuitive Google style free text search or using the Mammalian Phenotype (MP) ontology tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database.11712Mon, 20 May 2013 11:00:20 -0400 http://polybrowse.abcc.ncifcrf.gov/MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database currently includes polymorphisms identified from our alignment of whole-genome shotgun sequence traces from four laboratory mouse strains mapped against the reference C57BL/6J genome using GMAP. They can be queried on a local level by chromosomal coordinates, nearby gene names or other genomic feature identifiers, or in bulk format using categories including mouse strain(s), class of polymorphism(s) and chromosome number. The results of such queries are presented either as a custom track on the UCSC mouse genome browser or in tabular format.11713Sun, 19 May 2013 11:30:23 -0400 http://www.ncbi.nlm.nih.govThe National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.11618Mon, 20 May 2013 12:00:22 -0400 http://www.gene.affrc.go.jp/databases_en.phpThe National Institute of Agrobiological Sciences Genebank Project database (NIASGBdb) consists of a genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database has plant and microorganism search systems to provide information on research materials, including passport and evaluation data for genetic resources with the desired properties. A database of plant diseases in Japan has been developed based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan. Relevant plant and microorganism genetic resources are associated with the plant disease names.11910Fri, 17 May 2013 17:40:27 -0400 http://www.cls.zju.edu.cn/pair/The predicted Arabidopsis interactome resource (PAIR) contains experimentally reported molecular interactions and predicted interactions in Arabidopsis thaliana. PAIR predicts interactions by a fine-tuned support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). PAIR features a user-friendly query interface, providing rich annotation on the relationships between two proteins. A graphical interaction network browser has also been integrated into the PAIR web interface to facilitate mining of specific pathways.11913Mon, 20 May 2013 07:00:31 -0400 http://paramecium.cgm.cnrs-gif.frParameciumDB is a database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches.11908Sun, 19 May 2013 04:00:29 -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 12:20:31 -0400 http://www.pathwaycommons.orgPathway Commons is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data.11823Fri, 17 May 2013 12:20:26 -0400 http://www.peroxisomeDB.orgPeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae, as well as 35 newly sequenced eukaryotic genomes including fungi, yeasts, plants and lower eukaryotes. PeroxisomeDB 2.0 integrates the peroxisomal metabolome of whole microbody familiy by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana. The database includes phylogenetic trees and tools to capture kinetic information from Brenda, CheBI and Sabio-RK databases and selected bibliographic references.11742Sat, 18 May 2013 09:20:38 -0400 http://www.phenomicdb.dePhenomicDB a free multi-organism phenotype-genotype database unifying a variety of primary sources to make phenotypic data from a wide range of species and model organisms simultaneously searchable, visible and comparable. Gene orthology and similarity information mapped to particular entries, and the phenotypic data clustering system, provide facilities for the discovery of new phenotypic manifestations of a given genotype. Reported relationships are supported by evidence and reference links.13257Mon, 20 May 2013 14:00:23 -0400 http://pbil.univ-lyon1.fr/databases/pheverThe PhEVER database provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families.11797Mon, 20 May 2013 05:30:11 -0400 http://www.phisite.orgphiSITE is a database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central). 11674Mon, 20 May 2013 08:50:24 -0400 http://phosphat.mpimp-golm.mpg.de/The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.11746Sat, 18 May 2013 05:10:46 -0400 http://phylomeDB.orgPhylomeDB is a public database for genome-wide collections of gene phylogenies (phylomes). It is also a major source for phylogeny-based orthology and paralogy predictions. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana, but also alternative model species such as the human pathogen Candida albicans, or the pea aphid Acyrtosiphon pisum.11801Sat, 18 May 2013 06:20:22 -0400 http://cbg.garvan.unsw.edu.au/pina/Protein Interaction Network Analysis platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network. 13536Mon, 20 May 2013 01:50:36 -0400 http://bioinformatics.cau.edu.cn/PMRDThe plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. In some instances, miRNA expression profiles are included in the PMRD.11743Sun, 19 May 2013 17:30:14 -0400 http://www.prgdb.orgPRGdb is a database provides a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. Data can be examined using different query tools. A prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. The inferred cross-link between genomic and phenotypic information allows access to a large body of information.11744Sun, 19 May 2013 22:20:21 -0400 http://bis.zju.edu.cn/pnatdb/Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. Plant Natural Antisense Transcripts DataBase is a platform for annotating and discovering NATs by integrating various data sources. 13576Sat, 18 May 2013 09:40:31 -0400 http://planttfdb.cbi.pku.edu.cnThe PlantTFDB 2.0 plant transcription factor (TF) database contains detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to various databases and literature citations for these TFs. Multiple sequence alignments and phylogenetic trees for each family can be shown as Weblogo pictures or downloaded as text files.11787Tue, 14 May 2013 04:40:27 -0400 http://plntfdb.bio.uni-potsdam.de/The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.11745Tue, 14 May 2013 04:30:15 -0400 http://bis.zju.edu.cn/pmirkb/Plant miRNA knowledge base (PmiRKB) provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subspecies were collected to inspect the SNPs within pre-miRNAs (precursor microRNAs) and miRNA-target RNA duplexes. A second module, 'Pri-miR', can be used to investigate the tissue-specific, transcriptional contexts of pre- and pri-miRNAs (primary microRNAs), based on massively parallel signature sequencing data. The third module, 'MiR-Tar', was designed to validate thousands of miRNA-target pairs by using parallel analysis of RNA end (PARE) data. The fourth module, 'Self-reg', also used PARE data to investigate the metabolism of miRNA precursors, including precursor processing and miRNA- or miRNA*-mediated self-regulation effects on their host precursors.11937Mon, 20 May 2013 08:40:10 -0400 http://pre.ensembl.org/index.htmlThe Ensembl pre-build site provides displays of genomes that are in the process of being annotated. 13379Mon, 20 May 2013 03:00:17 -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.11741Sun, 19 May 2013 10:20:25 -0400 http://proportal.mit.edu/A database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus.13508Mon, 20 May 2013 11:10:07 -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://redfly.ccr.buffalo.eduThe REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.11901Sat, 18 May 2013 13:30:27 -0400 http://regprecise.lbl.govThe RegPrecise database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.11635Mon, 20 May 2013 00:10:07 -0400 http://regulondb.ccg.unam.mx/RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.11848Mon, 20 May 2013 13:40:31 -0400 http://ricexpro.dna.affrc.go.jp/RiceXPro is a gene expression database to provide the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes.11860Sun, 19 May 2013 10:00:10 -0400 http://scinets.org/db/mammalThe RIKEN integrated database of mammals integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. The integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations.11800Thu, 16 May 2013 14:20:33 -0400 http://salad.dna.affrc.go.jp/salad/en/SALAD is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available.11747Fri, 17 May 2013 18:40:36 -0400 http://scld.mcb.uconn.eduThe Stem Cell Lineage Database (SCLD) user-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.11891Thu, 16 May 2013 16:00:26 -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.11685Mon, 20 May 2013 03:20:07 -0400 http://silkworm.genomics.org.cn/The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.11689Sat, 18 May 2013 20:50:19 -0400 http://solgenomics.net/The Sol Genomics Network (SGN) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools.11920Sun, 19 May 2013 14:20:23 -0400 http://soybase.orgSoyBase, the soybean genetic database, is a comprehensive repository for curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.11748Sun, 19 May 2013 11:50:14 -0400 http://arabidopsis.org/The Arabidopsis Information Resource (TAIR): genome database for Arabidopsis thaliana. Central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. 13578Mon, 20 May 2013 01:00:34 -0400 http://catfishgenome.orgThe catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. 11921Sun, 19 May 2013 08:50:20 -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.11619Sun, 19 May 2013 05:20:23 -0400 http://ted.bti.cornell.eduTomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences.11897Wed, 15 May 2013 20:50:40 -0400 http://www.TriTrypDB.orgTriTrypDB is an integrated database providing access to genome-scale datasets for kinetoplastid parasites. TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a search strategy system that enables a user to construct complex queries combining multiple data types. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search.11690Thu, 16 May 2013 16:10:22 -0400 http://genome.ucsc.edu/The University of California, Santa Cruz (UCSC) Genome Browser website provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. Genomic sequence and a basic set of annotation 'tracks' are provided for organisms, including mammals, non-mammal vertebrates, invertebrate deuterostomes, insects, worms and yeast. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.11715Sun, 19 May 2013 19:50:25 -0400 http://www.vectorbase.org/A NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. Hosts data for nine genomes: mosquitoes, tick, body louse, kissing bug, and tsetse fly. Data includes genome features, expression data, population genetics, and ontologies.13521Sun, 19 May 2013 06:10:14 -0400 http://www.mgc.ac.cn/VFs/Virulence Factor Database: comprehensive repository of bacterial virulence factors. 13509Sun, 19 May 2013 21:20:21 -0400 http://www.viralorfeome.com/ViralORFeome 1.0 is a database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale.11675Fri, 17 May 2013 23:00:28 -0400 http://www.expasy.org/viralzone/ViralZone web resource provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. ViralZone offers a complete set of detailed and accurate virion pictures.11916Sat, 18 May 2013 07:20:22 -0400 http://www.wormbase.orgWormBase is a data repository for nematode biology. WormBase has expanded to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes.11691Sat, 18 May 2013 14:00:45 -0400 http://www.xenbase.orgXenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. Xenbase collaborates with the European Xenopus Research Center (EXRC) to provide a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and for Xenopus gene nomenclature.11714Sat, 18 May 2013 19:40:26 -0400 http://www.yeastract.comThe YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. EASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches. 11893Mon, 20 May 2013 04:00:12 -0400 http://www.ymdb.ca/Yeast Metabolome Database: a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). 13531Sun, 19 May 2013 19:30:21 -0400 http://ypa.ee.ncku.edu.tw/The Yeast Promoter Atlas (YPA) database collects promoter features in Saccharomyces cerevisiae. YPA integrates nine kinds of promoter features including promoter sequences, genes' transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5'-UTRs) and three prime untranslated regions (3'UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction. In YPA, various promoter features can be accessed in a centralized and organized platform.11866Sun, 19 May 2013 21:10:18 -0400 http://zfin.orgZFIN, the Zebrafish Model Organism Database serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations.11880Sun, 19 May 2013 03:10:14 -0400 http://zfishbook.org/Database of revertible protein trap gene-breaking transposon (GBT) insertional mutants in the zebrafish Danio rerio. 13542Mon, 20 May 2013 05:40:16 -0400