Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene

被引：9

作者：

Hobolth, A

Jensen, JL

机构：

[1] Univ Aarhus, Bioinformat Res Ctr, DK-8000 Aarhus, Denmark

[2] Univ Aarhus, Dept Theoret Stat & MaPhySto, DK-8000 Aarhus, Denmark

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2005年 / 12卷 / 02期

关键词：

alignment; comparative genomics; EM-algorithm; gene finding; hidden Markov model; phylogeny; structure prediction;

D O I：

10.1089/cmb.2005.12.186

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Identifying and characterizing the structure in genome sequences is one of the principal challenges in modern molecular biology, and comparative genomics offers a powerful tool. In this paper, we introduce a hidden Markov model that allows a comparative analysis of multiple sequences related by a phylogenetic tree, and we present an efficient method for estimating the parameters of the model. The model integrates structure prediction methods for one sequence, statistical multiple alignment methods, and phylogenetic information. This unified model is particularly useful for a detailed characterization of DNA sequences with a common gene. We illustrate the model on a variety of homologous sequences.

引用

页码：186 / 203

页数：18

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