Posted by: shrikantmantri | October 6, 2009

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-b…

via Bioinformatics on 10/3/09


Publication Date: 2009 Oct 1 PMID: 19797408
Authors: Jin, V. X. – Apostolos, J. – Nagisetty, N. S. – Farnham, P. J.
Journal: Bioinformatics

SUMMARY: 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 through-put 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: 1) we have refined the p-value with a Bonferroni correction; 2) 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. AVAILABILITY: http://motif.bmi.ohio-state.edu/ChIPMotifs CONTACT: victor.jin@osumc.edu SUPPLEMENTARY INFORMATION: Data used in the paper may be downloaded from <a href="http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml.
http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml.<br />
post to: CiteULike

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