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

Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Genome, Human
  • Humans
  • Protein Binding
  • Sequence Analysis, DNA / methods*
  • Software*


  • Chromatin
  • DNA-Binding Proteins