A comprehensive database and comparison platform for pseudogene annotation

John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul Harrrison, Mark Gerstein

Research output: Contribution to journalArticlepeer-review

140 Scopus citations


The knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different approaches to the problem of identification. Consequently, it is difficult to maintain a consistent collection of pseudogenes in detail necessary for their effective use. Our database is designed to address this issue. It integrates a variety of heterogeneous resources and supports a subset structure that highlights specific groups of pseudogenes that are of interest to the research community. Tools are provided for the comparison of sets and the creation of layered set unions, enabling researchers to derive a current 'consensus' set of pseudogenes. Additional features include versatile search, the capacity for robust interaction with other databases, the ability to reconstruct older versions of the database (accounting for changing genome builds) and an underlying object-oriented interface designed for researchers with a minimal knowledge of programming. At the present time, the database contains more than 100 000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources.

Original languageEnglish (US)
Pages (from-to)D55-D60
JournalNucleic acids research
Issue numberSUPPL. 1
StatePublished - Jan 2007
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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