Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2007 35(Database issue):D55-D60; doi:10.1093/nar/gkl851
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Nucleic Acids Research, 2007, Vol. 35, Database issue D55-D60
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
Center for Comparative Genomics and Bioinformatics 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA 1 Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA 2 Banting and Best Department of Medical Research (BBDMR), Donnelly CCBR University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1 3 Department of Computer Science, Yale University New Haven, CT 06520, USA 4 Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, QC, Canada H3A 1B1 5 Program in Computational Biology and Bioinformatics, Yale University Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
*To whom correspondence should be addressed. Tel: +1 814 865 4747; Fax: +1 814 863 6699; Email: jkarro{at}acm.org
Received February 23, 2006. Revised October 6, 2006. Accepted October 10, 2006.
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.
Correspondence may also be addressed to Mark Gerstein. Tel: +1 203 432 6105; Fax: +1 203 432 5175; Email: Mark.Gerstein{at}yale.edu
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