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Genome Biol. 2006;7 Suppl 1:S13.1-10. Epub 2006 Aug 7.

A computational approach for identifying pseudogenes in the ENCODE regions.

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  • 1Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT 06520, USA.

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.

PMID:
16925835
[PubMed - indexed for MEDLINE]
PMCID:
PMC1810550
Free PMC Article

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