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Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

SUMMARY: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species. AVAILABILITY: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software.

Pubmed ID: 20562413 RIS Download

Mesh terms: Genetic Variation | Genomics | Internet | Polymorphism, Single Nucleotide | Software

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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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