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Nucleic Acids Research 2005 33(10):3263-3270; doi:10.1093/nar/gki644
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Published online 7 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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, please contact journals.permissions{at}oupjournals.org

Article

Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming

Pål Sætrom*, Ragnhild Sneve1, Knut I. Kristiansen1, Ola Snøve, Jr, Thomas Grünfeld, Torbjørn Rognes1 and Erling Seeberg1

Interagon AS, Medisinsk teknisk senter NO-7489 Trondheim, Norway 1Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet University Hospital NO-0027 Oslo, Norway

*To whom correspondence should be addressed. Tel: +47 9820 3874; Fax: +47 4559 4458; Email: paal.saetrom{at}interagon.com

Received November 24, 2004. Revised February 22, 2005. Accepted May 20, 2005.

Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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