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Estimation of alternative splicing isoform frequencies from RNA-Seq data

Authors Marius Nicolae, Serghei Mangul, Ion Mandoiu, Alex Zelikovsky



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Marius Nicolae
Serghei Mangul
Ion Mandoiu
Alex Zelikovsky

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Marius Nicolae, Serghei Mangul, Ion Mandoiu, and Alex Zelikovsky. Estimation of alternative splicing isoform frequencies from RNA-Seq data. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2010)
https://doi.org/10.4230/DagSemProc.10231.5

Abstract

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 largely ignored 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.
Keywords
  • RNA-Seq
  • alternative splicing isoforms
  • expectation maximization

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