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Bioinformatics Advance Access published online on March 30, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl116
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 28, 2005
Revised March 1, 2006
Accepted March 22, 2006

Article

PseudoPipe: an automated pseudogene identification pipeline

Zhaolei Zhang 1, Nicholas Carriero 2, Deyou Zheng 3, John Karro 4, Paul M. Harrison 5, and Mark Gerstein 3 *

1 Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
2 Department of Computer Science, Yale University, New Haven, CT 06520, USA
3 Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA
4 Department of Biology, 506 Wartik, Penn. State University, University Park, PA 16802, USA
5 Department of Biology, McGill University, Stewart Biology Building, 1205 Dr. Penfield Ave., Montreal, QC, H3A 1B1, Canada

* To whom correspondence should be addressed.
Mark Gerstein, E-mail: Mark.Gerstein{at}yale.edu


  Abstract

Motivation: Mammalian genomes contain many "genomcic fossils" i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes.

Results: We have developed a homology-based computational pipeline ("PseudoPipe") that can search a mammalian genome and identify pseudogene sequences in a comprehensive and consistent manner. Pseudogenes are classified based on a combination of criteria including sequence homology, intron and exon structure, existence of stop codons and frameshifts, and other sequence features. This pipeline has been used to assign pseudogenes in a uniform and comparable fashion in a number of vertebrate genomes, including those of the human, mouse, rat, chimpanzee, chicken and dog.

Availability: The PseudoPipe program is implemented in Python and can be downloaded at http://pseudogene.org/.

Associate Editor: Keith A Crandall
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