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Ensembl 2013.

Nucleic acids research | Jan 20, 2013

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Pubmed ID: 23203987 RIS Download

Mesh terms: Animals | Databases, Genetic | Gene Expression Regulation | Genetic Variation | Genomics | Humans | Internet | Mice | Molecular Sequence Annotation | Rats | Software | Zebrafish

Research resources used in this publication

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Research tools detected in this publication

Data used in this publication

None found

Associated grants

  • Agency: Biotechnology and Biological Sciences Research Council, Id: BB/I025506/1
  • Agency: Biotechnology and Biological Sciences Research Council, Id: BB/E011640/1
  • Agency: NHGRI NIH HHS, Id: U01HG004695
  • Agency: NHGRI NIH HHS, Id: U41HG006104
  • Agency: NHGRI NIH HHS, Id: U54HG004563
  • Agency: Wellcome Trust, Id: WT079643
  • Agency: Wellcome Trust, Id: WT062023
  • Agency: Wellcome Trust, Id: 095908
  • Agency: NHGRI NIH HHS, Id: U54 HG004555

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Ensembl

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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European Bioinformatics Institute

A non-profit academic organization for research and services in bioinformatics that provides freely available data from life science experiments, performs basic research in computational biology, and offers an extensive user training programme, supporting researchers in academia and industry. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures.

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