HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.

ABSTRACT:

Background

Protein-DNA interaction constitutes a basic mechanism for the genetic regulation of target gene expression. Deciphering this mechanism has been a daunting task due to the difficulty in characterizing protein-bound DNA on a large scale. A powerful technique has recently emerged that couples chromatin immunoprecipitation (ChIP) with next-generation sequencing, (ChIP-Seq). This technique provides a direct survey of the cistrom of transcription factors and other chromatin-associated proteins. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed to analyze the massive amount of data generated by this method.

Results

Here we introduce HPeak, a Hidden Markov model (HMM)-based Peak-finding algorith

SUBMITTER: Qin ZS 

PROVIDER: S-EPMC2912305 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature