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Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.

Publication ,  Journal Article
Ohler, U; Niemann, H; Liao Gc, ; Rubin, GM
Published in: Bioinformatics
2001

We present an approach to integrate physical properties of DNA, such as DNA bendability or GC content, into our probabilistic promoter recognition system McPROMOTER. In the new model, a promoter is represented as a sequence of consecutive segments represented by joint likelihoods for DNA sequence and profiles of physical properties. Sequence likelihoods are modeled with interpolated Markov chains, physical properties with Gaussian distributions. The background uses two joint sequence/profile models for coding and non-coding sequences, each consisting of a mixture of a sense and an anti-sense submodel. On a large Drosophila test set, we achieved a reduction of about 30% of false positives when compared with a model solely based on sequence likelihoods.

Duke Scholars

Published In

Bioinformatics

DOI

ISSN

1367-4803

Publication Date

2001

Volume

17 Suppl 1

Start / End Page

S199 / S206

Location

England

Related Subject Headings

  • Stochastic Processes
  • Promoter Regions, Genetic
  • Neural Networks, Computer
  • Models, Statistical
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Drosophila
  • Databases, Nucleic Acid
  • DNA
 

Citation

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MLA
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Ohler, U., Niemann, H., Liao Gc, ., & Rubin, G. M. (2001). Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics, 17 Suppl 1, S199–S206. https://doi.org/10.1093/bioinformatics/17.suppl_1.s199
Ohler, U., H. Niemann, H. Liao Gc, and G. M. Rubin. “Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.Bioinformatics 17 Suppl 1 (2001): S199–206. https://doi.org/10.1093/bioinformatics/17.suppl_1.s199.
Ohler U, Niemann H, Liao Gc, Rubin GM. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics. 2001;17 Suppl 1:S199–206.
Ohler, U., et al. “Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.Bioinformatics, vol. 17 Suppl 1, 2001, pp. S199–206. Pubmed, doi:10.1093/bioinformatics/17.suppl_1.s199.
Ohler U, Niemann H, Liao Gc, Rubin GM. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics. 2001;17 Suppl 1:S199–S206.
Journal cover image

Published In

Bioinformatics

DOI

ISSN

1367-4803

Publication Date

2001

Volume

17 Suppl 1

Start / End Page

S199 / S206

Location

England

Related Subject Headings

  • Stochastic Processes
  • Promoter Regions, Genetic
  • Neural Networks, Computer
  • Models, Statistical
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Drosophila
  • Databases, Nucleic Acid
  • DNA