title: AVISPA: a web tool for the prediction and analysis of alternative splicing.
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.
authors.forename: Yoseph
authors.initials: Y
authors.lastname: Barash
authors.forename: Jorge
authors.initials: J
authors.lastname: Vaquero-Garcia
authors.forename: Juan
authors.initials: J
authors.lastname: González-Vallinas
authors.forename: Hui Yuan
authors.initials: HY
authors.lastname: Xiong
authors.forename: Weijun
authors.initials: W
authors.lastname: Gao
authors.forename: Leo J
authors.initials: LJ
authors.lastname: Lee
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Frey
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D005091:Exons; D023281:Genomics / Q000379:methods; D009928:Organ Specificity / Q000235:genetics; D012372:ROC Curve; D059467:Transcriptome; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics; D064878:Web Browser
chemical_list: D042461:Vascular Endothelial Growth Factor A