Nucleic Acids Research, 2005, Vol. 33, Database issue D59-D66
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
HOPPSIGEN: a database of human and mouse processed pseudogenes
Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard–Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
* To whom correspondence should be addressed. Tel: +33 472 43 35 82; Fax: +33 478 89 27 19; Email: khelifi{at}biomserv.univ-lyon1.fr
Received August 10, 2004; Revised and Accepted October 12, 2004
Processed pseudogenes result from reverse transcribed mRNAs. In general, because processed pseudogenes lack promoters, they are no longer functional from the moment they are inserted into the genome. Subsequently, they freely accumulate substitutions, insertions and deletions. Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes. Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution. Recently, there is an increasing interest for these markers, particularly to help gene prediction in the field of genome annotation, functional genomics and genome evolution analysis (patterns of substitution). For these reasons, we have developed a method to annotate processed pseudogenes in complete genomes. To make them useful to different fields of research, we stored them in a nucleic acid database after having annotated them. In this work, we screened both mouse and human complete genomes from ENSEMBL to find processed pseudogenes generated from functional genes with introns. We used a conservative method to detect processed pseudogenes in order to minimize the rate of false positive sequences. Within processed pseudogenes, some are still having a conserved open reading frame and some have overlapping gene locations. We designated as retroelements all reverse transcribed sequences and more strictly, we designated as processed pseudogenes, all retroelements not falling in the two former categories (having a conserved open reading or overlapping gene locations). We annotated 5823 retroelements (5206 processed pseudogenes) in the human genome and 3934 (3428 processed pseudogenes) in the mouse genome. Compared to previous estimations, the total number of processed pseudogenes was underestimated but the aim of this procedure was to generate a high-quality dataset. To facilitate the use of processed pseudogenes in studying genome structure and evolution, DNA sequences from processed pseudogenes, and their functional reverse transcribed homologs, are now stored in a nucleic acid database, HOPPSIGEN. HOPPSIGEN can be browsed on the PBIL (Pôle Bioinformatique Lyonnais) World Wide Web server (http://pbil.univ-lyon1.fr/) or fully downloaded for local installation.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J.-F. Lucier, J. Perreault, J.-F. Noel, G. Boire, and J.-P. Perreault RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures Nucleic Acids Res., July 13, 2007; 35(suppl_2): W269 - W274. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, A. Reymond, S. W. Choo, Y. Lu, F. Denoeud, S. E. Antonarakis, M. Snyder, et al. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution Genome Res., June 1, 2007; 17(6): 839 - 851. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting, P. Harrrison, and M. Gerstein Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation Nucleic Acids Res., January 12, 2007; 35(suppl_1): D55 - D60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Yao, R. Charlab, and P. Li Systematic identification of pseudogenes through whole genome expression evidence profiling Nucleic Acids Res., September 11, 2006; 34(16): 4477 - 4485. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Drouin Processed Pseudogenes Are More Abundant in Human and Mouse X Chromosomes than in Autosomes Mol. Biol. Evol., September 1, 2006; 23(9): 1652 - 1655. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. SZYMANSKI and J. BARCISZEWSKI RNA regulation in mammals. Ann. N.Y. Acad. Sci., May 1, 2006; 1067: 461 - 468. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Meunier, A. Khelifi, V. Navratil, and L. Duret Homology-dependent methylation in primate repetitive DNA PNAS, April 12, 2005; 102(15): 5471 - 5476. [Abstract] [Full Text] [PDF]
|
|