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Authors: Anna A. Nilulova 1 ; Alexander V. Favorov 2 ; Vsevolod Yu. Makeev 3 and Andrey A. Mironov 1

Affiliations: 1 Moscow State University and Russian Academy of Sciences, Russian Federation ; 2 School of Medicine, Johns Hopkins University and Russian Academy of Sciences, United States ; 3 Russian Academy of Sciences, Russian Federation

ISBN: 978-989-8425-90-4

Keyword(s): Generalized hidden markov models, Regulation of transcription, Cis-regulatory modules, Binding sites, Regulatory structure, Eukaryotes.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis

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 transcri ptional regulation mechanisms in higher eukaryotes. (More)

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Paper citation in several formats:
A. Nilulova, A.; V. Favorov, A.; Yu. Makeev, V. and A. Mironov, A. (2012). A GENERALIZED HIDDEN MARKOV MODEL FOR PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTE GENOMES AND DESCRIPTION OF THEIR INTERNAL STRUCTURE.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 34-41. DOI: 10.5220/0003735800340041

@conference{bioinformatics12,
author={Anna A. Nilulova. and Alexander V. Favorov. and Vsevolod Yu. Makeev. and Andrey A. Mironov.},
title={A GENERALIZED HIDDEN MARKOV MODEL FOR PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTE GENOMES AND DESCRIPTION OF THEIR INTERNAL STRUCTURE},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={34-41},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003735800340041},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - A GENERALIZED HIDDEN MARKOV MODEL FOR PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTE GENOMES AND DESCRIPTION OF THEIR INTERNAL STRUCTURE
SN - 978-989-8425-90-4
AU - A. Nilulova, A.
AU - V. Favorov, A.
AU - Yu. Makeev, V.
AU - A. Mironov, A.
PY - 2012
SP - 34
EP - 41
DO - 10.5220/0003735800340041

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