Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/89869
Citations
Scopus Web of Science® Altmetric
?
?
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.
Zhang, D.
Citation: BMC Bioinformatics, 2010; 11(1):81-1-81-8
Publisher: BioMed Central
Issue Date: 2010
ISSN: 1471-2105
1471-2105
Statement of
Responsibility: 
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 (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
RMID: 0030023477
DOI: 10.1186/1471-2105-11-81
Appears in Collections:Agriculture, Food and Wine publications

Files in This Item:
File Description SizeFormat 
hdl_89869.pdfPublished version570.99 kBAdobe PDFView/Open


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.