title: ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.
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).
authors.affiliation: Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fullwood
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Fabianus Hendriyan
authors.initials: FH
authors.lastname: Mulawadi
authors.forename: Stoyan
authors.initials: S
authors.lastname: Velkov
authors.forename: Vinsensius
authors.initials: V
authors.lastname: Vega
authors.forename: Pramila Nuwantha
authors.initials: PN
authors.lastname: Ariyaratne
authors.forename: Yusoff Bin
authors.initials: YB
authors.lastname: Mohamed
authors.forename: Hong-Sain
authors.initials: HS
authors.lastname: Ooi
authors.forename: Chandana
authors.initials: C
authors.lastname: Tennakoon
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D015894:Genome, Human; D006801:Humans; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins