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

Created by W.Langdon from gp-bibliography.bib Revision:1.4524

  title =        "Predicting non-coding {RNA} genes in Escherichia coli
                 with boosted genetic programming",
  author =       "Pal Saetrom and Ragnhild Sneve and 
                 Knut I. Kristiansen and Ola Snove and Thomas Grunfeld and 
                 Torbjorn Rognes and Erling Seeberg",
  year =         "2005",
  journal =      "Nucleic Acids Research",
  volume =       "33",
  number =       "10",
  pages =        "3263--3270",
  month =        jun # "~08",
  bibsource =    "OAI-PMH server at",
  language =     "en",
  oai =          "",
  rights =       "{\copyright} The Author 2005. Published by Oxford
                 University Press. All rights reserved",
  keywords =     "genetic algorithms, genetic programming",
  URL =          "",
  URL =          "",
  URL =          "",
  DOI =          "doi:10.1093/nar/gki644",
  size =         "8 pages",
  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
  notes =        "Included in \cite{drphil-satrom-05}

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

                 Cited by High-Throughput, Kingdom-Wide Prediction and
                 Annotation of Bacterial Non-Coding RNAs Jonathan Livny,
                 Hidayat Teonadi, Miron Livny, and Matthew K. Waldor
                 PLoS ONE. 2008; 3(9): e3197.

                 Biocomputational prediction of small non-coding RNAs in
                 Streptomyces Josef Panek, Jan Bobek, Karel Mikulik,
                 Marek Basler, and Ji?i Vohradsky BMC Genomics. 2008; 9:
                 217. Published online 2008 May 13.
                 doi:10.1186/1471-2164-9-217. PMCID:

                 Identification of chromosomal alpha-proteobacterial
                 small RNAs by comparative genome analysis and detection
                 in Sinorhizobium meliloti strain 1021 Vincent M Ulve,
                 Emeric W Sevin, Angelique Cheron, and Frederique
                 Barloy-Hubler BMC Genomics. 2007; 8: 467. Published
                 online 2007 December 19. doi:10.1186/1471-2164-8-467.
                 PMCID: PMC2245857",

Genetic Programming entries for Pal Saetrom Ragnhild Sneve Knut Ivan Kristiansen Ola Snove Jr Thomas Grunfeld Torbjorn Rognes Erling Seeberg