A generalized hidden Markov model for prediction of cis-regulatory modules in eukaryote genomes and description of their internal structure

Anna A. Nilulova, Alexander Favorov, Vsevolod Yu Makeev, Andrey A. Mironov

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Eukaryotic regulatory regions have been studied extensively due to their importance for gene regulation in higher eukaryotes. However, the understanding of their organization is clearly incomplete. In particular, we lack accurate in silico methods for their prediction. Here we present a new HMM-based method for the prediction of regulatory regions in eukaryotic genomes using position weight matrices of the relevant transcription factors. The method reveals and then utilizes the regulatory region structure (preferred binding site arrangements) to increase the quality of the prediction, as well as to provide a new knowledge of the regulatory region organization. We show that our method can be successfully used for the identification of regulatory regions in eukaryotic genomes with a quality higher than that of other methods. We also demonstrate the ability of our algorithm to reveal structural features of the regulatory regions, which could be helpful for the deciphering of the transcriptional regulation mechanisms in higher eukaryotes.

Original languageEnglish (US)
Title of host publicationBIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
Pages34-41
Number of pages8
Publication statusPublished - 2012
EventInternational Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2012 - Vilamoura, Algarve, Portugal
Duration: Feb 1 2012Feb 4 2012

Other

OtherInternational Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2012
CountryPortugal
CityVilamoura, Algarve
Period2/1/122/4/12

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Keywords

  • Binding sites
  • Cis-regulatory modules
  • Eukaryotes
  • Generalized hidden Markov models
  • Regulation of transcription
  • Regulatory structure

ASJC Scopus subject areas

  • Modeling and Simulation

Cite this

Nilulova, A. A., Favorov, A., Makeev, V. Y., & Mironov, A. A. (2012). A generalized hidden Markov model for prediction of cis-regulatory modules in eukaryote genomes and description of their internal structure. In BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (pp. 34-41)