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.
Buck, M. J., Nobel, A. B., & Lieb, J. D. (2005). ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biology, 6(11). https://doi.org/10.1186/gb-2005-6-11-r97