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MBE Advance Access published online on August 17, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi238
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted August 4, 2005

Research Article

Statistical Alignment of Retropseudogenes and Their Functional Paralogs

Miklós Csrös 1* and István Miklós 2

1 Department of Computer Science and Operations Research, Université de Montréal, C. P. 6128, succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada. Phone: +1 (514) 343-6111 ext. 1655, Fax: +1 (514) 343-5834
2 Department of Plant Taxonomy and Ecology, Eötvös Lóránd University, 1117 Budapest, Pázmány Péter Sétány 1/c, Hungary

* To whom correspondence should be addressed.
Miklós Csrös, E-mail: csuros{at}iro.umontreal.ca


  Abstract

We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions and deletions, and combines nucleotide- and codon-level mutation models. We give a dynamic programming method for calculating the likelihood of homology between two sequences in the model, and describe the accompanying alignment algorithm. We also describe how ancestral codons can be computed when the same gene produced multiple pseudogene homologs. We apply our methods to the evolution of human cytochrome c.

Keywords: molecular evolution; pairwise sequence alignment; processed pseudogenes; Thorne-Kishino-Felsenstein model; cytochrome c.
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