PseudoPipe: an automated pseudogene identification pipeline.
BACKGROUND
Mammalian genomes contain many 'genomic 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. The key steps in the pipeline involve using BLAST to rapidly cross-reference potential "parent" proteins against the intergenic regions of the genome and then processing the resulting "raw hits" -- i.e. eliminating redundant ones, clustering together neighbors, and associating and aligning clusters with a unique parent. Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts.
Zhang
Zhaolei
Z
Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada.
Carriero
Nicholas
N
Zheng
Deyou
D
Karro
John
J
Harrison
Paul M
PM
Gerstein
Mark
M
D000465:Algorithms; D000818:Animals; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D011544:Pseudogenes; D015203:Reproducibility of Results; D012984:Software