Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data

In this paper we present a novel expectation-maximization algorithm for inference of alternative splicing isoform frequencies from high-throughput transcriptome sequencing (RNA-Seq) data. Our algorithm exploits disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information if available. Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data. The Java implementation of IsoEM is available at http://dna.engr.uconn.edu/software/IsoEM/.

• Type: Journal
• Year: 2010
• Where: WABI
• Authors: Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky
• Keywords: Algorithm Exploits Disambiguation, Bioinformatics, Expression Level Estimation, Splicing Isoform Frequencies, WABI 2010