DPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.

ABSTRACT: Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) has been successfully used for genome-wide profiling of transcription factor binding sites, histone modifications, and nucleosome occupancy in many model organisms and humans. Because the compact genomes of prokaryotes harbor many binding sites separated by only few base pairs, applications of ChIP-Seq in this domain have not reached their full potential. Applications in prokaryotic genomes are further hampered by the fact that well studied data analysis methods for ChIP-Seq do not result in a resolution required for deciphering the locations of nearby binding events. We generated single-end tag (SET) and paired-end tag (PET) ChIP-Seq data for σ⁷⁰ factor in Escherichia coli (E. coli). Direct comparison of these

SUBMITTER: Chung D 

PROVIDER: S-EPMC3798280 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature