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

• DOI: 10.1007/978-1-61779-400-1_20
• Publication Date: 2011-12-02T11:27:34Z
• Authors: Leelavati Narlikar; Raja Jothi
• Keywords: Chromatin immunoprecipitation; ChIP-sequencing; Identification; Immunoprecipitation

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.