title: Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.
abstract: 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.
authors.affiliation: Bioinformatics Program, School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
authors.forename: Ao
authors.initials: A
authors.lastname: Zhou
authors.forename: Marcus R
authors.initials: MR
authors.lastname: Breese
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Hao
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Edenberg
authors.forename: Lang
authors.initials: L
authors.lastname: Li
authors.forename: Todd C
authors.initials: TC
authors.lastname: Skaar
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Liu
mesh_terms: D000438:Alcohols / Q000494:pharmacology; D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D030541:Databases, Genetic; D005091:Exons; D016678:Genome; D006801:Humans; D008099:Liver / Q000187:drug effects / Q000378:metabolism; D012313:RNA / Q000378:metabolism*; D051381:Rats; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D000438:Alcohols; D012313:RNA