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A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure

  • Liran Carmel
  • Igor B. Rogozin
  • Yuri I. Wolf
  • Eugene V. Koonin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 541)

Abstract

Spliceosomal introns are one of the principal distinctive features of eukaryotes. Nevertheless, different large-scale studies disagree about even the most basic features of their evolution. In order to come up with a more reliable reconstruction of intron evolution, we developed a model that is far more comprehensive than previous ones. This model is rich in parameters, and estimating them accurately is infeasible by straightforward likelihood maximization. Thus, we have developed an expectation-maximization algorithm that allows for efficient maximization. Here, we outline the model and describe the expectation-maximization algorithm in detail. Since the method works with intron presence–absence maps, it is expected to be instrumental for the analysis of the evolution of other binary characters as well.

Key words

Maximum likelihood expectation-maximization intron evolution ancestral reconstruction eukaryotic gene structure 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

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 Medicine, National Institutes of HealthBethesdaUSA

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