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

@article{citeulike:237591, abstract = {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.}, address = {Interagon AS, Medisinsk teknisk senter NO-7489 Trondheim, Norway. paal.saetrom@interagon.com}, author = {Saetrom, P. and Sneve, R. and Kristiansen, K. I. and Snøve, O. and Gr\"{u}nfeld, T. and Rognes, T. and Seeberg, E. }, citeulike-article-id = {237591}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {genes, genetic, non-coding, programming, rna}, number = {10}, pages = {3263--3270}, posted-at = {2005-06-25 13:03:58}, priority = {2}, title = {Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/15942029}, volume = {33}, year = {2005} }

TY - JOUR ID - citeulike:237591 L3 - citeulike-article-id:237591 TI - Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. JF - Nucleic Acids Res VL - 33 IS - 10 SP - 3263 EP - 3270 AD - Interagon AS, Medisinsk teknisk senter NO-7489 Trondheim, Norway. paal.saetrom@interagon.com SN - 1362-4962 N2 - 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. KW - genes KW - genetic KW - non-coding KW - programming KW - rna AU - Saetrom, P AU - Sneve, R AU - Kristiansen, KI AU - Snøve, O AU - Grünfeld, T AU - Rognes, T AU - Seeberg, E PY - 2005/// UR - http://view.ncbi.nlm.nih.gov/pubmed/15942029 ER -