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Nucleic Acids Research Advance Access published online on May 16, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn294
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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QUMA: quantification tool for methylation analysis

Yuichi Kumaki, Masaaki Oda and Masaki Okano*

Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan

*To whom correspondence should be addressed. Tel: +81 78 306 3164; Fax: +81 78 306 3167; Email: okano{at}cdb.riken.jp

Correspondence may also be addressed to Yuichi Kumaki. Tel: +81 78 306 3166; Fax: +81 78 306 3167; Email: kuma{at}cdb.riken.jp

Received January 28, 2008. Revised April 18, 2008. Accepted April 29, 2008.

Bisulfite sequencing, a standard method for DNA methylation profile analysis, is widely used in basic and clinical studies. This method is limited, however, by the time-consuming data analysis processes required to obtain accurate DNA methylation profiles from the raw sequence output of the DNA sequencer, and by the fact that quality checking of the results can be influenced by a researcher's bias. We have developed an interactive and easy-to-use web-based tool, QUMA (quantification tool for methylation analysis), for the bisulfite sequencing analysis of CpG methylation. QUMA includes most of the data-processing functions necessary for the analysis of bisulfite sequences. It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/.

Present address: Masaaki Oda, Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK


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