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Databases

This section contains databases of model organism genomes, vertebrate/non-vertebrate/plant/organelle genomes, and taxonomy/identification.

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Found 94 links

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AgBaseDatabase Content

http://www.agbase.msstate.edu/

Model Organisms > Databases

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.

NAR Database Issue 2011
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tagsagricultural crops agriculture animals cats dogs domestic animals gene expression profiling genetic databases genetic models genomics oligonucleotide array sequence analysis

AGRISDatabase Content

http://arabidopsis.med.ohio-state.edu/

Model Organisms > Databases

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.

NAR Database Issue 2011
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tagsarabidopsis gene regulatory networks genetic databases genetic promoter regions plant gene expression regulation transcription factors

AHD2.0Database Content

http://ahd.cbi.pku.edu.cn/

Model Organisms > Databases

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.

NAR Database Issue 2011
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tagsarabidopsis genetic databases micrornas plant genes plant growth regulators rna splicing

AmoebaDB and MicrosporidiaDBDatabase Content

http://AmoebaDB.org

Model Organisms > Databases

AmoebaDB 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.

NAR Database Issue 2011
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tagsencephalitozoon entamoeba fungal genome genetic databases genomics protozoan genome

ArachnoServer 2.0Database Content

http://www.arachnoserver.org

Model Organisms > Databases
Protein > Databases

ArachnoServer 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.

This content is being maintained by glennfking.

NAR Database Issue 2011
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tagsanimals protein databases proteins sequence analysis spider venoms spiders

AspGDDatabase Content

http://www.aspergillusgenome.org/

Model Organisms > Databases

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.

NAR Database Issue 2010
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tagsaspergillus nidulans computational biology fungal genes fungal genome fungal proteins genetic databases genetic models genetics nucleic acid databases phenotype protein databases tertiary protein structure

AtPIDDatabase Content

http://www.megabionet.org/atpid/

Model Organisms > Databases
Protein > Databases

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.

NAR Database Issue 2011
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tagsarabidopsis proteins molecular sequence annotation protein databases protein interaction mapping proteomics

BeetleBaseDatabase Content

http://beetlebase.org/

Model Organisms > Databases

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.

NAR Database Issue 2010
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tagsanimals computational biology expressed sequence tags genetic databases genetic models genome genomics nucleic acid databases protein databases tertiary protein structure tribolium

BgeeDatabase Content

http://bgee.unil.ch/

Expression > Databases
Model Organisms > Databases

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.

This content is being maintained by bgee.

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tagsanatomical ontology anatomy bgee development developmental ontology evo-devo database evolution gene expression gene expression evolution' ontology

Bovine Genome DatabaseDatabase Content

http://BovineGenome.org

Model Organisms > Databases

The 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.

NAR Database Issue 2011
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tagsanimals cattle genetic databases genetic models genome genomics molecular sequence annotation quantitative trait loci sequence alignment systems integration

CAMERADatabase Content

http://camera.calit2.net/

Model Organisms > Databases

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.

NAR Database Issue 2011
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tagsenvironment genetic databases metagenome metagenomics

Candida Genome DatabaseDatabase Content

http://www.candidagenome.org/

Model Organisms > Databases

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.

NAR Database Issue 2010
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tagscandida albicans computational biology fungal dna fungal genes fungal genome genetic databases nucleic acid databases open reading frames protein databases tertiary protein structure

CiFDatabase Content

http://www.fusariumdb.org/

Model Organisms > Databases

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.

NAR Database Issue 2011
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tagsfungal genome fungal proteins fusarium genetic databases genomics multigene family phylogeny systems integration

CIPRO 2.5Database Content

http://cipro.ibio.jp/2.5

Model Organisms > Databases

The 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.

NAR Database Issue 2011
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tagsamino acid sequence animals ciona intestinalis computational biology gene expression profiling genomics molecular sequence annotation protein databases proteome proteomics systems integration

COMBREXDatabase Content

http://combrex.bu.edu

Model Organisms > Databases

COMBREX 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.

NAR Database Issue 2011
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tagsarchaeal genome bacterial genome genetic databases genomics molecular sequence annotation protein databases

Tags associated with subcategory 'Model Organisms/Databases'

genetic databases computational biology protein databases animals nucleic acid databases genomics tertiary protein structure humans genetic polymorphism molecular models inbred strains mice programming languages invertebrates chromosomes cryopreservation gene expression species specificity xenopus laevis inbred c57bl mice automation xenopus plant genome knockout mice multigene family bombyx cell line nucleic acid probes drosophila melanogaster rna interference trypanosoma leishmania genetic variation mice search engine single nucleotide polymorphism caenorhabditis elegans caenorhabditis University of Toronto factual databases molecular imaging phosphorylation phosphoproteins phosphoserine protein sequence analysis plant proteins gene regulatory networks phosphopeptides genetic markers algorithms bacteriophages biology plant chromosomes soybeans quantitative trait loci oxidative stress plant diseases dna primers base sequence polymerase chain reaction drosophila proteins mammalian embryo virus diseases peroxisomes peroxisomal disorders micrornas plant genes plant gene expression regulation plants metabolomics metabolome mutation genetic transcription archaeal genome systems biology genome bacterial genes amino acid motifs controlled vocabulary protein interaction mapping pharmaceutical preparations viral genes open reading frames viral gene expression regulation fungal genome ligands human genome bacterial genome binding sites systems integration phylogeny united states viral genome sequence analysis proteins nucleic acids gene expression profiling operon dna sequence alignment transcription factors European Bioinformatics Institute (EBI)