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Bioinformatics Advance Access originally published online on October 1, 2009
Bioinformatics 2009 25(23):3191-3193; doi:10.1093/bioinformatics/btp570
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Victor X. Jin 1,*, Jeff Apostolos 1, Naga Satya Venkateswara Ra Nagisetty 2 and Peggy J. Farnham 3

1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, 2 Bioinformatics Program, The University of Memphis, Memphis, TN 38152 and 3 The Genome Center, The University of California, Davis, CA 95616, USA

* To whom correspondence should be addressed.


  Abstract

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-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.

Availability: 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.

Contact: victor.jin{at}osumc.edu

Associate Editor: Martin Bishop

Received on August 3, 2009; revised on September 28, 2009; accepted on September 29, 2009

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