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QUMA: QUantification tool for Methylation Analysis
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You can easily align, visualize and quantify
bisulfite sequence data for CpG methylation analysis

 list  Overview: how to use QUMA space  list  Quick start space  list  Execute with sample sequence data space  list  Sample sequence files
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 list  Upload target genomic sequence (PCR target) file
(plain sequence, FASTA or GenBank format)
The genomic sequence must be an unconverted sequence between PCR primer pair (not necessary to convert "C" to "T").
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 list  Upload bisulfite sequence file
(multi-FASTA format file or zipped archive of sequence files)
Raw sequence data can be used. Removal of plasmid vector sequence is not necessary.
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help
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 arrow    Show options
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    Supported browsers
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We support the following web browsers;
  • Firefox (Mac/Win)
  • Safari (Mac)
  • Opera (Mac/Win)
  • Internet Explorer(IE) 6.0 and higher (Win)  (IE 7 is not recommended because it has many bugs)
Many browsers such as IE 5.0 for Windows, Mozilla, and Netscape 6 and higher may work as well.
Some older browsers such as IE for Mac or Netscape 4 will not work.
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    Contact information
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  Yuichi Kumaki & Masaki Okano
  Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN
  2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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    What's New
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  • May 16, 2008   new
  • May 2, 2008
    • More options about CpG positions added to the function of making methylation pattern figure
    • Function of addition/replacemnt of bisulfite seqeunces is added to the result page of the methylation status analysis mode
    • Manuscript of QUMA has been accepted by NAR
    • Download files updated
    • "Links" section now available and "Acknowledgements" section was integrated into "Reference" section
  • Apr 21, 2008
    • CpG postision number bug of the methylation pattern figure fixed
    • Typos fixed
  • Apr 17, 2008
    • "Download" section now available
      • Program source code of the QUMA now available
      • LiveCD (bootable CD) version of the QUMA now available
    • QUMA User's Manual updated
    • New "Show CpG position" option added to the function of making methylation pattern figure
    • New sorting condition "sequence name" added, "How to use" section updated, some online helps added, site structure changed, some descriptions changed and some minor functions added.
    • Implementation of Mann-Whiteney U-test is changed: now using exact test for small number of seqeunces (20 and below).
  • Mar 31, 2008
    • The last line truncation bug of the multi-fasta sequence input is fixed.
  • Feb 21, 2008
    • "Terms of Use" section now available
    • Minor bug fixed and "Acknowledgements" section updated
  • Feb 18, 2008
    • Typos fixed and "Acknowledgements" section updated
  • Jan 30, 2008
    • QUMA User's Manual now available
    • Typos fixed, "Acknowledgements" and "Reference" sections updated, and "What's New" column created
  • Updated at Nov 29 and 30, Dec 4, 5, 12, 13 and 14, 2007, Jan 04 and 17 2008
  • Nov 23, 2007
    • The QUMA web server now available

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spacer Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN
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spacer RIKEN
If you have any questions/comments/requests etc., please feel free to contact  : 
quma@cdb.riken.jp
Copyright© 2008 RIKEN Center for Developmental Biology All rights reserved.
Last updated at Sat May 17 15:51:38 JST 2008