ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder

Methods Mol Biol. 2012:802:305-22. doi: 10.1007/978-1-61779-400-1_20.


Protein-DNA interactions play key roles in determining gene-expression programs during cellular development and differentiation. Chromatin immunoprecipitation (ChIP) is the most widely used assay for probing such interactions. With recent advances in sequencing technology, ChIP-Seq, an approach that combines ChIP and next-generation parallel sequencing is fast becoming the method of choice for mapping protein-DNA interactions on a genome-wide scale. Here, we briefly review the ChIP-Seq approach for mapping protein-DNA interactions and describe the use of the SISSRs peak-finder, a software tool for precise identification of protein-DNA binding sites from sequencing data generated using ChIP-Seq.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms
  • Animals
  • Binding Sites / genetics
  • Chromatin Immunoprecipitation*
  • Computational Biology / methods
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Mice
  • Sequence Analysis, DNA / methods*
  • Software*


  • DNA-Binding Proteins
  • DNA