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This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) – Genomics

Open Access Research

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

Ao Zhou12, Marcus R Breese234, Yangyang Hao234, Howard J Edenberg2345, Lang Li246, Todd C Skaar6 and Yunlong Liu234*

Author Affiliations

1 Bioinformatics Program, School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA

2 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

3 Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

4 Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

5 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA

6 Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA

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BMC Genomics 2012, 13(Suppl 8):S10  doi:10.1186/1471-2164-13-S8-S10

Published: 17 December 2012

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.