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ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Guoliang Li1†, Melissa J Fullwood2†, Han Xu1†, Fabianus Hendriyan Mulawadi1, Stoyan Velkov1, Vinsensius Vega1, Pramila Nuwantha Ariyaratne1, Yusoff Bin Mohamed1, Hong-Sain Ooi1, Chandana Tennakoon3, Chia-Lin Wei2, Yijun Ruan2,4* and Wing-Kin Sung1,3*

Author Affiliations

1 Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Republic of Singapore

2 Genomic Technologies, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Republic of Singapore

3 Department of Computer Science, School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Republic of Singapore

4 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore

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Genome Biology 2010, 11:R22 doi:10.1186/gb-2010-11-2-r22

Published: 25 February 2010

Abstract

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg webcite).