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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

13 Scopus citations

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.

Original languageAmerican English
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages35-46
Number of pages12
DOIs
StatePublished - 2005
Externally publishedYes
EventRECOMB 2005 International Workshop on Comparative Genomics, RCG 2005 - Dublin, Ireland
Duration: 18 Sep 200520 Sep 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3678 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceRECOMB 2005 International Workshop on Comparative Genomics, RCG 2005
Country/TerritoryIreland
CityDublin
Period18/09/0520/09/05

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