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Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

BACKGROUND: Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splic...

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Detalles Bibliográficos
Autores principales: Zhou, Ao, Breese, Marcus R, Hao, Yangyang, Edenberg, Howard J, Li, Lang, Skaar, Todd C, Liu, Yunlong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535697/
https://www.ncbi.nlm.nih.gov/pubmed/23281921
http://dx.doi.org/10.1186/1471-2164-13-S8-S10
Descripción
Sumario:BACKGROUND: Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing. RESULTS: We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure. CONCLUSIONS: Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.