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Interpolated markov chains for eukaryotic promoter recognition.

Publication ,  Journal Article
Ohler, U; Harbeck, S; Niemann, H; Nöth, E; Reese, MG
Published in: Bioinformatics
May 1999

MOTIVATION: We describe a new content-based approach for the detection of promoter regions of eukaryotic protein encoding genes. Our system is based on three interpolated Markov chains (IMCs) of different order which are trained on coding, non-coding and promoter sequences. It was recently shown that the interpolation of Markov chains leads to stable parameters and improves on the results in microbial gene finding (Salzberg et al., Nucleic Acids Res., 26, 544-548, 1998). Here, we present new methods for an automated estimation of optimal interpolation parameters and show how the IMCs can be applied to detect promoters in contiguous DNA sequences. Our interpolation approach can also be employed to obtain a reliable scoring function for human coding DNA regions, and the trained models can easily be incorporated in the general framework for gene recognition systems. RESULTS: A 5-fold cross-validation evaluation of our IMC approach on a representative sequence set yielded a mean correlation coefficient of 0.84 (promoter versus coding sequences) and 0.53 (promoter versus non-coding sequences). Applied to the task of eukaryotic promoter region identification in genomic DNA sequences, our classifier identifies 50% of the promoter regions in the sequences used in the most recent review and comparison by Fickett and Hatzigeorgiou ( Genome Res., 7, 861-878, 1997), while having a false-positive rate of 1/849 bp.

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Published In

Bioinformatics

DOI

ISSN

1367-4803

Publication Date

May 1999

Volume

15

Issue

5

Start / End Page

362 / 369

Location

England

Related Subject Headings

  • Promoter Regions, Genetic
  • Markov Chains
  • Humans
  • Eukaryotic Cells
  • Electronic Data Processing
  • Drosophila melanogaster
  • DNA
  • Bioinformatics
  • Animals
  • Algorithms
 

Citation

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Ohler, U., Harbeck, S., Niemann, H., Nöth, E., & Reese, M. G. (1999). Interpolated markov chains for eukaryotic promoter recognition. Bioinformatics, 15(5), 362–369. https://doi.org/10.1093/bioinformatics/15.5.362
Ohler, U., S. Harbeck, H. Niemann, E. Nöth, and M. G. Reese. “Interpolated markov chains for eukaryotic promoter recognition.Bioinformatics 15, no. 5 (May 1999): 362–69. https://doi.org/10.1093/bioinformatics/15.5.362.
Ohler U, Harbeck S, Niemann H, Nöth E, Reese MG. Interpolated markov chains for eukaryotic promoter recognition. Bioinformatics. 1999 May;15(5):362–9.
Ohler, U., et al. “Interpolated markov chains for eukaryotic promoter recognition.Bioinformatics, vol. 15, no. 5, May 1999, pp. 362–69. Pubmed, doi:10.1093/bioinformatics/15.5.362.
Ohler U, Harbeck S, Niemann H, Nöth E, Reese MG. Interpolated markov chains for eukaryotic promoter recognition. Bioinformatics. 1999 May;15(5):362–369.
Journal cover image

Published In

Bioinformatics

DOI

ISSN

1367-4803

Publication Date

May 1999

Volume

15

Issue

5

Start / End Page

362 / 369

Location

England

Related Subject Headings

  • Promoter Regions, Genetic
  • Markov Chains
  • Humans
  • Eukaryotic Cells
  • Electronic Data Processing
  • Drosophila melanogaster
  • DNA
  • Bioinformatics
  • Animals
  • Algorithms