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space titile QUMA (QUantification tool for Methylation Analysis) top
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    Reference
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QUMA: quantification tool for methylation analysis

Yuichi Kumaki, Masaaki Oda & Masaki Okano*, Nucleic Acids Res. 36, W170-W175 (2008).
DOI:10.1093/nar/gkn294, PubMed Central ID: PMC2447804, PubMed ID: 18487274
Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN,
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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/.
*To whom correspondence should be addressed.
Correspondence may also be addressed to Yuichi Kumaki.
Present address for Masaaki Oda:
Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK
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    Acknowledgements
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We thank Akiko Yamagiwa for sample bisulfite sequences of the mouse Gm9 region1, Morito Sakaue and Masahumi Kawaguchi for constructive feedback on the website, Hazuki S. Hiraga for proofreading of the web site, Yoko Dote for helpful feedback on the "Terms of Use" section, and the Information Networks Office of RIKEN Kobe Institute for helpful suggestions in setting up the Internet connection for the server. This work was supported in part by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan to M. Okano.

We also thank the following software programs and web pages.

  1. DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner. Oda, M., Yamagiwa, A., Yamamoto, S., Nakayama, T., Tsumura, A., Sasaki, H., Nakao, K., Li, E. and Okano, M. Genes & Development, 20, 3382-3394 (2006).
  2. EMBOSS: The European Molecular Biology Open Software Suite. Rice,P., Longden,I. and Bleasby,A. Trends in Genetics, 16,276-277 (2000).

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