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

Michael J Buck1, Andrew B Nobel2 and Jason D Lieb1*

Author Affiliations

1 Department of Biology and Carolina Center for Genome Sciences, CB 3280, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA

2 Department of Statistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3260, USA

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Genome Biology 2005, 6:R97  doi:10.1186/gb-2005-6-11-r97

Published: 19 October 2005

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.