MOTIVATION: 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.
MOTIVATION: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.
Authors: Deyou Zheng; Adam Frankish; Robert Baertsch; Philipp Kapranov; Alexandre Reymond; Siew Woh Choo; Yontao Lu; France Denoeud; Stylianos E Antonarakis; Michael Snyder; Yijun Ruan; Chia-Lin Wei; Thomas R Gingeras; Roderic Guigó; Jennifer Harrow; Mark B Gerstein Journal: Genome Res Date: 2007-06 Impact factor: 9.043