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. 2010 Aug 15;26(16):2069-70.
doi: 10.1093/bioinformatics/btq330. Epub 2010 Jun 18.

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

William McLaren  1 , Bethan Pritchard, Daniel Rios, Yuan Chen, Paul Flicek, Fiona Cunningham
Affiliations

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

William McLaren et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
Consequence types predicted by Ensembl in the context of transcript structure. The other types shown apply to non-protein coding genes.
See this image and copyright information in PMC

References

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    1. Rios D, et al. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics. 2010;11:293. - PMC - PubMed
    1. Sherry ST, et al. dbSNP—database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999;9:677–679. - PubMed

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