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

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.

Pubmed ID: 22130889


  • Narlikar L
  • Jothi R


Methods in molecular biology (Clifton, N.J.)

Publication Data

December 1, 2012

Associated Grants

  • Agency: Intramural NIH HHS, Id: ZIA ES102625-02

Mesh Terms

  • Algorithms
  • Animals
  • Binding Sites
  • Chromatin Immunoprecipitation
  • Computational Biology
  • DNA
  • DNA-Binding Proteins
  • Humans
  • Mice
  • Sequence Analysis, DNA
  • Software