Next Generation Microarray Bioinformatics

Volume 802 of the series Methods in Molecular Biology pp 305-322


ChIP-Seq Data Analysis: Identification of Protein–DNA Binding Sites with SISSRs Peak-Finder

  • Leelavati NarlikarAffiliated withNational Institutes of Environmental Health Sciences, National Institutes of Health
  • , Raja JothiAffiliated withCentre for Modeling and Simulation, University of Pune Email author 

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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.

Key words

ChIP-Seq SISSRs Protein–DNA interaction Binding sites Transcription factor Next-generation sequencing Genomics