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

Methods Mol Biol. 2012;802:305-22

Authors: Narlikar L, Jothi R

Abstract
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.


PMID: 22130889 [PubMed - in process]



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