Pseudogene.org

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 journalArticle

115 Citations (Scopus)

Abstract

The Pseudogene.org 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)
JournalNucleic Acids Research
Volume35
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2007
Externally publishedYes

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Pseudogenes
Databases
Research Personnel
Genome
Public Opinion
Knowledge Bases
Eukaryota
Research

ASJC Scopus subject areas

  • Genetics

Cite this

Pseudogene.org : A comprehensive database and comparison platform for pseudogene annotation. / Karro, John E.; Yan, Yangpan; Zheng, Deyou; Zhang, Zhaolei; Carriero, Nicholas; Cayting, Philip; Harrrison, Paul; Gerstein, Mark.

In: Nucleic Acids Research, Vol. 35, No. SUPPL. 1, 01.2007.

Research output: Contribution to journalArticle

Karro, JE, Yan, Y, Zheng, D, Zhang, Z, Carriero, N, Cayting, P, Harrrison, P & Gerstein, M 2007, 'Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation', Nucleic Acids Research, vol. 35, no. SUPPL. 1. https://doi.org/10.1093/nar/gkl851
Karro, John E. ; Yan, Yangpan ; Zheng, Deyou ; Zhang, Zhaolei ; Carriero, Nicholas ; Cayting, Philip ; Harrrison, Paul ; Gerstein, Mark. / Pseudogene.org : A comprehensive database and comparison platform for pseudogene annotation. In: Nucleic Acids Research. 2007 ; Vol. 35, No. SUPPL. 1.
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