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

William McLaren; Bethan Pritchard; Daniel Rios; Yuan Chen; Paul Flicek; Fiona Cunningham

doi:10.1093/bioinformatics/btq330

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

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

Authors

William McLaren¹, Bethan Pritchard, Daniel Rios, Yuan Chen, Paul Flicek, Fiona Cunningham

Affiliation

¹ European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. wm2@ebi.ac.uk

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genetic Variation*
Genomics*
Internet
Polymorphism, Single Nucleotide*
Software*

Grants and funding

Wellcome Trust/United Kingdom