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

A. Zhou, Marcus R. Breese, Yangyang Hao, Howard Edenberg, Lang Li, Todd Skaar, Yunlong Liu

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

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. 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. 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.

Original languageEnglish (US)
Article numberS10
JournalBMC Genomics
Volume13 Suppl 8
StatePublished - 2012
Externally publishedYes

Fingerprint

Alternative Splicing
Human Genome
Proteome
Exons
Protein Isoforms
Alcohols
Genome
RNA
Liver
Genes

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Alt Event Finder : a tool for extracting alternative splicing events from RNA-seq data. / Zhou, A.; Breese, Marcus R.; Hao, Yangyang; Edenberg, Howard; Li, Lang; Skaar, Todd; Liu, Yunlong.

In: BMC Genomics, Vol. 13 Suppl 8, S10, 2012.

Research output: Contribution to journalArticle

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