An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes

  • Liran Carmel
  • Igor B. Rogozin
  • Yuri I. Wolf
  • Eugene V. Koonin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3678)

Abstract

We propose a detailed model of evolution of exon-intron structure of eukaryotic genes that takes into account gene-specific intron gain and loss rates, branch-specific gain and loss coefficients, invariant sites incapable of intron gain, and rate variability of both gain and loss which is gamma-distributed across sites. We develop an expectation-maximization algorithm to estimate the parameters of this model, and study its performance using simulated data.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Liran Carmel
    • 1
  • Igor B. Rogozin
    • 1
  • Yuri I. Wolf
    • 1
  • Eugene V. Koonin
    • 1
  1. 1.National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaUSA

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