使用系统发育隐马尔可夫模型在果蝇中寻找顺式调控模块。

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.

作者信息

Wong Wendy S W, Nielsen Rasmus

机构信息

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

出版信息

Bioinformatics. 2007 Aug 15;23(16):2031-7. doi: 10.1093/bioinformatics/btm299. Epub 2007 Jun 5.

DOI:10.1093/bioinformatics/btm299

PMID:17550911

Abstract

MOTIVATION

Finding the regulatory modules for transcription factors binding is an important step in elucidating the complex molecular mechanisms underlying regulation of gene expression. There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data.

RESULTS

We develop a method for finding regulatory modules in Eukaryotic species using phylogenetic data. Using computer simulations and analysis of real data, we show that the use of phylogenetic hidden Markov model can lead to an increase in accuracy of prediction over methods that do not take advantage of the data from multiple species.

AVAILABILITY

The new method is made accessible under GPL in a new publicly available JAVA program: EvoPromoter. It can be downloaded at http://sourceforge.net/projects/evopromoter/.

摘要