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Genome Biol. 2005;6(11):R97. Epub 2005 Oct 19.

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

Author information

  • 1Department of Biology, Carolina Center for Genome Sciences, CB 3280, University of North Carolina, Chapel Hill, NC 27599-3280, USA. mjbuck@bio.unc.edu

Abstract

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.

PMID:
16277752
[PubMed - indexed for MEDLINE]
PMCID:
PMC1297653
Free PMC Article

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