An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

Background: ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites. Results: Here, we present SIPeS (Site Identification from Paired-end Sequencing), a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS), which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS. Conclusions: When compared t...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson, Dabing Zhang
• Keywords: Binding Sites, BMCBI 2010, Chromatin Immunoprecipitation, SIPeS