A computational approach for identifying pseudogenes in the ENCODE regions

Genome Biol. 2006;7 Suppl 1(Suppl 1):S13.1-10. doi: 10.1186/gb-2006-7-s1-s13. Epub 2006 Aug 7.

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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Genomics / methods*
  • Pseudogenes*
  • Sequence Analysis, DNA
  • Software