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

Barash, Yoseph; Vaquero-Garcia, Jorge; González-Vallinas Rostes, Juan, 1983-; Xiong, Hui Yuan; Gao, Weijun; Lee, Leo J.; Frey, Brendan J.

doi:http://dx.doi.org/10.1186/gb-2013-14-10-r114

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

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Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY Gao W, Lee LJ, et al. AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biol. 2013;14:R114. DOI: 10.1186/gb-2013-14-10-r114

Abstract

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.