AVISPA: a web tool for the prediction and analysis of alternative splicing

被引：29

作者：

Barash, Yoseph ^{[1
,2
,4
,5
]}

Vaquero-Garcia, Jorge ^{[1
,2
]}

Gonzalez-Vallinas, Juan ^{[1
,3
]}

Xiong, Hui Yuan ^{[4
]}

Gao, Weijun ^{[4
]}

Lee, Leo J. ^{[4
]}

Frey, Brendan J. ^{[4
,5
]}

机构：

[1] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA

[2] Univ Penn, Dept Comp & Informat Sci, Philadelphia, PA 19104 USA

[3] Univ Pompeu Fabra, Barcelona 08003, Spain

[4] Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada

[5] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5G 1L6, Canada

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 10期

基金：

加拿大自然科学与工程研究理事会;

关键词：

TRANSCRIPTOME; PROTEINS; SEQUENCE; MOTIFS;

D O I：

10.1186/gb-2013-14-10-r114

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Transcriptome complexity and its relation to numerous diseases underpins the need to predict in silico splice variants and the regulatory elements that affect them. Building upon our recently described splicing code, we developed AVISPA, a Galaxy-based web tool for splicing prediction and analysis. Given an exon and its proximal sequence, the tool predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. We assess AVISPA's accuracy on an independent dataset of tissue-dependent exons, and illustrate how the tool can be applied to analyze a gene of interest. AVISPA is available at http://avispa.biociphers.org.

引用

页数：8

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