A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure.

Liran Carmel*, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

5 Scopus citations

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.

Original languageAmerican English
Pages (from-to)357-371
Number of pages15
JournalMethods in Molecular Biology
Volume541
DOIs
StatePublished - 2009
Externally publishedYes

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