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

被引：1265

作者：

McLaren, William ^{[1
]}

Pritchard, Bethan ^{[2
]}

Rios, Daniel ^{[1
]}

Chen, Yuan ^{[1
]}

Flicek, Paul ^{[1
]}

Cunningham, Fiona ^{[1
]}

机构：

[1] European Bioinformat Inst, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

BIOINFORMATICS | 2010年 / 26卷 / 16期

基金：

英国惠康基金;

关键词：

D O I：

10.1093/bioinformatics/btq330

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2069 / 2070

页数：2

共 5 条

[1] Ensembl variation resources [J].

Chen, Yuan ;

Cunningham, Fiona ;

Rios, Daniel ;

McLaren, William M. ;

Smith, James ;

Pritchard, Bethan ;

Spudich, Giulietta M. ;

Brent, Simon ;

Kulesha, Eugene ;

Marin-Garcia, Pablo ;

Smedley, Damian ;

Birney, Ewan ;

Flicek, Paul .

BMC GENOMICS, 2010, 11

[2] Ensembl's 10th year [J].

Flicek, Paul ;

Aken, Bronwen L. ;

Ballester, Benoit ;

Beal, Kathryn ;

Bragin, Eugene ;

Brent, Simon ;

Chen, Yuan ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Fernandez-Banet, Julio ;

Gordon, Leo ;

Graef, Stefan ;

Haider, Syed ;

Hammond, Martin ;

Howe, Kerstin ;

Jenkinson, Andrew ;

Johnson, Nathan ;

Kaehaeri, Andreas ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Kokocinski, Felix ;

Koscielny, Gautier ;

Kulesha, Eugene ;

Lawson, Daniel ;

Longden, Ian ;

Massingham, Tim ;

McLaren, William ;

Megy, Karine ;

Overduin, Bert ;

Pritchard, Bethan ;

Rios, Daniel ;

Ruffier, Magali ;

Schuster, Michael ;

Slater, Guy ;

Smedley, Damian ;

Spudich, Giulietta ;

Tang, Y. Amy ;

Trevanion, Stephen ;

Vilella, Albert ;

Vogel, Jan ;

White, Simon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D557-D562

[3] Next generation tools for the annotation of human SNPs [J].

Karchin, Rachel .

BRIEFINGS IN BIOINFORMATICS, 2009, 10 (01) :35-52

[4] A database and API for variation, dense genotyping and resequencing data [J].

Rios, Daniel ;

McLaren, William M. ;

Chen, Yuan ;

Birney, Ewan ;

Stabenau, Arne ;

Flicek, Paul ;

Cunningham, Fiona .

BMC BIOINFORMATICS, 2010, 11

[5]

Sherry ST, 1999, GENOME RES, V9, P677

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