title: ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.
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.
authors: National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
authors: Leelavati
authors: L
authors: Narlikar
authors: Raja
authors: R
authors: Jothi
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA