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Type: Journal article
Title: An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Author: Wang, C.
Xu, J.
Zhang, D.
Wilson, Z.A.
Zhang, D.
Citation: BMC Bioinformatics, 2010; 11(1):81-1-81-8
Publisher: BioMed Central
Issue Date: 2010
ISSN: 1471-2105
Statement of
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, and Dabing Zhang
Abstract: 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 to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.
Keywords: DNA-Binding Proteins
Rights: © 2010 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI: 10.1186/1471-2105-11-81
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