Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Software

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

Yoseph Barash1245*, Jorge Vaquero-Garcia12, Juan González-Vallinas13, Hui Yuan Xiong4, Weijun Gao4, Leo J Lee4 and Brendan J Frey45

Author Affiliations

1 Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA

2 Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA

3 Universitat Pompeu Fabra, Barcelona 08003, Spain

4 Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada

5 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada

For all author emails, please log on.

Genome Biology 2013, 14:R114  doi:10.1186/gb-2013-14-10-r114

Published: 24 October 2013

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. AVISPA is available at http://avispa.biociphers.org webcite.