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Found 17 result(s)

Online Mendelian Inheritance in Animals

OMIA

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Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 218 animal species (other than human and mouse and rats, which have their own resources) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. OMIA information is stored in a database that contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI, and to OMIM and Ensembl.

Animal QTLdb

Animal Quantitative Trait Loci

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This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called "QTL data" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

Database of Genomic Variants Archive

DGVa

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<<<!!!<<< Phasing out support for the Database of Genomic Variants archive (DGVa). The submission, archiving, and presentation of structural variation services offered by the DGVa is transitioning to the European Variation Archive (EVA) https://www.re3data.org/repository/r3d100011553. All of the data shown in the DGVa website is already searchable and browsable from the EVA Study Browser. Submission of structural variation data to EVA is done using the VCF format. The VCF specification allows representing multiple types of structural variants such as insertions, deletions, duplications and copy-number variants. Other features such as symbolic alleles, breakends, confidence intervals etc., support more complex events, such as translocations at an imprecise position. >>>!!!>>>

Viral Bioinformatics Resource Center

VBRC

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Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

Complete Genomics

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Complete Genomics provides free public access to a variety of whole human genome data sets generated from Complete Genomics’ sequencing service. The research community can explore and familiarize themselves with the quality of these data sets, review the data formats provided from our sequencing service, and augment their own research with additional summaries of genomic variation across a panel of diverse individuals. The quality of these data sets is representative of what a customer can expect to receive for their own samples. This public genome repository comprises genome results from both our Standard Sequencing Service (69 standard, non-diseased samples) and the Cancer Sequencing Service (two matched tumor and normal sample pairs). In March 2013 Complete Genomics was acquired by BGI-Shenzhen , the world’s largest genomics services company. BGI is a company headquartered in Shenzhen, China that provides comprehensive sequencing and bioinformatics services for commercial science, medical, agricultural and environmental applications. Complete Genomics is now focused on building a new generation of high-throughput sequencing technology and developing new and exciting research, clinical and consumer applications.

DNA Data Bank of Japan

DDBJ

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DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

The Comprehensive Resource of Mammalian protein complexes

CORUM

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CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

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This is a animal and human genome database that uses the BioMart software.

PeanutBase

Genetic and genomic data to enable more rapid crop improvement in peanut

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PeanutBase is a peanut community resource providing genetic, genomic, gene function, and germplasm data to support peanut breeding and molecular research. This includes molecular markers, genetic maps, QTL data, genome assemblies, germplasm records, and traits. Data is curated from literature and submitted directly by researchers. Funding for PeanutBase is provided by the Peanut Foundation with in-kind contributions from the USDA-ARS.

ArkDB

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<<<!!!<<< The ArkDB is now CLOSED With apologies to anyone who still relies on the ArkDB data system or map-drawing tools, we've had to take the difficult decision to shut down the ArkDB system. We've not been funded to maintain it for many years now and have kept it in the air as best we could with the time that we had available but recent changes in personnel and continuing updates to the underpinning libraries mean that the effort required to keep it going outweighs the perceived benefits. If you feel that this is the wrong decision, please contact us to let us know and we'll see what we can do together You can always contact us on our Roslin Bioinformatics email address (roslin.bioinformatics@roslin.ed.ac.uk) The Roslin Bioinformatics Team 21st November 2018 >>>!!!>>>

NAGRP Blast Center

National Animal Genome Research Program Blast Center

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NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.

1000 Genomes

Thousand Genomes

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The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies. The genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide. The International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.

EchoBase

an integrated post-genomic database for E.coli

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EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

Kyoto Encyclopedia of Genes and Genomes

KEGG

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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies