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

Bioinformatics - Tập 26 Số 16 - Trang 2069-2070 - 2010
William McLaren1, Bethan Yates1, Daniel Ríos1, Yuan Chen1, Paul Flicek1, Fiona Cunningham1
11 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

Tóm tắt

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.

Contact:  [email protected]; [email protected]

Supplementary information:  Supplementary data are available at Bioinformatics online.

Từ khóa


Tài liệu tham khảo

Chen, 2010, Ensembl variation resources, BMC Genomics, 11, 238, 10.1186/1471-2164-11-293

Flicek, 2010, Ensembl's 10th year, Nucleic Acids Res., 38, D557, 10.1093/nar/gkp972

Karchin, 2008, Next generation tools for the annotation of human SNPs, Brief Bioinformatics, 10, 35, 10.1093/bib/bbn047

Rios, 2010, A database and API for variation, dense genotyping and resequencing data, BMC Bioinformatics, 11, 293, 10.1186/1471-2105-11-238

Sherry, 1999, dbSNP—database for single nucleotide polymorphisms and other classes of minor genetic variation, Genome Res., 9, 677, 10.1101/gr.9.8.677

Thông tin
Thông tin xuất bản

Bioinformatics

Tập 26 Số 16

2069-2070

Thông tin tác giả