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URN: urn:nbn:de:0030-drops-26876
URL: http://drops.dagstuhl.de/opus/volltexte/2010/2687/

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

Estimation of alternative splicing isoform frequencies from RNA-Seq data

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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.

BibTeX - Entry

@InProceedings{nicolae_et_al:DSP:2010:2687,
  author =	{Marius Nicolae and Serghei Mangul and Ion Mandoiu and Alex Zelikovsky},
  title =	{Estimation of alternative splicing isoform frequencies from RNA-Seq data},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks & Phylogenies},
  year =	{2010},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  number =	{10231},
  series =	{Dagstuhl Seminar Proceedings},
  ISSN =	{1862-4405},
  publisher =	{Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2010/2687},
  annote =	{Keywords: RNA-Seq, alternative splicing isoforms, expectation maximization}
}

Keywords: RNA-Seq, alternative splicing isoforms, expectation maximization
Seminar: 10231 - Structure Discovery in Biology: Motifs, Networks & Phylogenies
Issue date: 2010
Date of publication: 04.08.2010


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