Feb 242013
 

IsoEM 1.1.1

:: DESCRIPTION

IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses a novel expectation-maximization algorithm that exploits read 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

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

IsoEM

:: MORE INFORMATION

Citation:

M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky,
Estimation of alternative splicing isoform frequencies from RNA-Seq data,
Algorithms for Molecular Biology , pp. to appear, 2011

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