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

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@Article{oai:pubmedcentral.gov:1143698,
  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 www.pubmedcentral.gov",
  language =     "en",
  oai =          "oai:pubmedcentral.gov:1143698",
  rights =       "{\copyright} The Author 2005. Published by Oxford
                 University Press. All rights reserved",
  keywords =     "genetic algorithms, genetic programming",
  URL =          "http://nar.oxfordjournals.org/cgi/reprint/33/10/3263.pdf",
  URL =          "http://www.pubmedcentral.gov/articlerender.fcgi?artid=1143698",
  URL =          "http://www.pubmedcentral.gov/picrender.fcgi?artid=1143698&blobtype=pdf",
  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
                 estimated.",
  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,
                 Norway

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}

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

Citations