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

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• dc.contributor.author Barash, Yoseph
• dc.contributor.author Vaquero-Garcia, Jorge
• dc.contributor.author González-Vallinas Rostes, Juan, 1983-
• dc.contributor.author Xiong, Hui Yuan
• dc.contributor.author Gao, Weijun
• dc.contributor.author Lee, Leo J.
• dc.contributor.author Frey, Brendan J.
• dc.date.accessioned 2023-06-27T06:16:30Z
• dc.date.available 2023-06-27T06:16:30Z
• dc.date.issued 2013
• dc.description.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.
• dc.format.mimetype application/pdf
• dc.identifier.citation 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
• dc.identifier.doi http://dx.doi.org/10.1186/gb-2013-14-10-r114
• dc.identifier.issn 1474-760X
• dc.identifier.uri http://hdl.handle.net/10230/57353
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biology. 2013;14:R114
• dc.rights © 2013 Barash et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/2.0
• dc.subject.keyword Differential inclusion
• dc.subject.keyword UCSC genome browser
• dc.subject.keyword Alternative exon
• dc.subject.keyword Nucleosome occupancy
• dc.subject.keyword Exon array
• dc.title AVISPA: a web tool for the prediction and analysis of alternative splicing
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion