W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.

Abstract

W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the program in two aspects: (i) we have refined the P-value with a Bonferroni correction; (ii) we have incorporated the STAMP tool to infer phylogenetic information and to determine the detected motifs if they are novel and known using the TRANSFAC and JASPAR databases. A comprehensive result file is mailed to users. http://motif.bmi.ohio-state.edu/ChIPMotifs. Data used in the article may be downloaded from http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml.