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A computational approach for identifying pseudogenes in the ENCODE regions.

Deyou Zheng·Mark B Gerstein
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Abstract

BACKGROUND: Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying them, which in contrast to previous work explicitly uses intron-exon structure in parent genes to classify pseudogenes. We require alignments between duplicated pseudogenes and their parents to span intron-exon junctions, and this can be used to distinguish between true duplicated and processed pseudogenes (with insertions). RESULTS: Applying our approach to the ENCODE regions, we identify about 160 pseudogenes, 10% of which have clear 'intron-exon' structure and are thus likely generated from recent duplications. CONCLUSION: Detailed examination of our results and comparison of our annotation with the GENCODE reference annotation demonstrate that our computation pipeline provides a good balance between identifying all pseudogenes and delineating the precise structure of duplicated genes.

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Computational BiologyGenomicsPseudogenesSequence Analysis, DNASoftwareComparative StudyEvaluation StudyJournal ArticleResearch Support, N.I.H., Extramural

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Deyou Zheng, Mark B Gerstein. 2006-08-07. A computational approach for identifying pseudogenes in the ENCODE regions.. https://doi.org/10.1186/gb-2006-7-s1-s13

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