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This article is part of the supplement: EGASP '05: ENCODE Genome Annotation Assessment Project

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A computational approach for identifying pseudogenes in the ENCODE regions

Deyou Zheng1 and Mark B Gerstein123*

Author Affiliations

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

2 Department of Computer Science, Yale University, Prospect Street, New Haven, CT 06520, USA

3 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

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Genome Biology 2006, 7(Suppl 1):S13  doi:10.1186/gb-2006-7-s1-s13

Published: 7 August 2006



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).


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.


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.