Next Generation Microarray Bioinformatics pp 305-322

Part of the Methods in Molecular Biology book series (MIMB, volume 802)

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.

Key words

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

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.National Institutes of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUSA
  2. 2.Centre for Modeling and SimulationUniversity of PunePuneIndia

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