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. 1992 Jul 11;20(13):3471–3477. doi: 10.1093/nar/20.13.3471

Escherichia coli promoters: neural networks develop distinct descriptions in learning to search for promoters of different spacing classes.

M C O'Neill 1
PMCID: PMC312504  PMID: 1630917

Abstract

Back-propagation neural networks were trained to recognize promoter sequences of each of the three major spacing classes found in E. coli. These networks were trained with the object of maximizing their ability to generalize while maintaining the level of false positive identifications at a fraction of 1 percent. These objectives were generally met. Networks for the 16 base spacing class captured between 78 and 100% of previously unseen promoters in different tests; networks for the 17 base class identified 97% of the test promoters; networks for the 18 base class identified 79% of the test promoters. A tandem poll of networks for all three spacing classes produced a cumulative false positive level of less than 0.5%. In each case, the weight matrices used by the networks in their classification were analyzed to determine the relative weight assigned to the occurrence of a given base at a given position within the promoter. In this fashion, an approximate description of the network's definition of the promoter can be obtained.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Brunner M., Bujard H. Promoter recognition and promoter strength in the Escherichia coli system. EMBO J. 1987 Oct;6(10):3139–3144. doi: 10.1002/j.1460-2075.1987.tb02624.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Demeler B., Zhou G. W. Neural network optimization for E. coli promoter prediction. Nucleic Acids Res. 1991 Apr 11;19(7):1593–1599. doi: 10.1093/nar/19.7.1593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Harley C. B., Reynolds R. P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Knaus R., Bujard H. PL of coliphage lambda: an alternative solution for an efficient promoter. EMBO J. 1988 Sep;7(9):2919–2923. doi: 10.1002/j.1460-2075.1988.tb03150.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lukashin A. V., Anshelevich V. V., Amirikyan B. R., Gragerov A. I., Frank-Kamenetskii M. D. Neural network models for promoter recognition. J Biomol Struct Dyn. 1989 Jun;6(6):1123–1133. doi: 10.1080/07391102.1989.10506540. [DOI] [PubMed] [Google Scholar]
  7. Moyle H., Waldburger C., Susskind M. M. Hierarchies of base pair preferences in the P22 ant promoter. J Bacteriol. 1991 Mar;173(6):1944–1950. doi: 10.1128/jb.173.6.1944-1950.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. O'Neill M. C. Consensus methods for finding and ranking DNA binding sites. Application to Escherichia coli promoters. J Mol Biol. 1989 May 20;207(2):301–310. doi: 10.1016/0022-2836(89)90256-8. [DOI] [PubMed] [Google Scholar]
  10. O'Neill M. C. Escherichia coli promoters. I. Consensus as it relates to spacing class, specificity, repeat substructure, and three-dimensional organization. J Biol Chem. 1989 Apr 5;264(10):5522–5530. [PubMed] [Google Scholar]
  11. O'Neill M. C. Training back-propagation neural networks to define and detect DNA-binding sites. Nucleic Acids Res. 1991 Jan 25;19(2):313–318. doi: 10.1093/nar/19.2.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Peden K. W. Revised sequence of the tetracycline-resistance gene of pBR322. Gene. 1983 May-Jun;22(2-3):277–280. doi: 10.1016/0378-1119(83)90112-9. [DOI] [PubMed] [Google Scholar]
  13. Schneider T. D., Stormo G. D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. doi: 10.1016/0022-2836(86)90165-8. [DOI] [PubMed] [Google Scholar]

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