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ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

http://www.ncbi.nlm.nih.gov/pubmed/22130889

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.

Pubmed ID: 22130889 RIS Download

Mesh terms: Algorithms | Animals | Binding Sites | Chromatin Immunoprecipitation | Computational Biology | DNA | DNA-Binding Proteins | Humans | Mice | Sequence Analysis, DNA | Software