You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis

Overview: how to use QUMA    Quick start    Execute with sample sequence data    Sample sequence files

Project name (optional: only contain "A-Z", "a-z", "0-9", "_" and "-")   :      Enter a target genomic sequence (PCR target) in plain sequence, FASTA or GenBank format

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"). or upload target genomic sequence (PCR target) file (plain sequence, FASTA or GenBank format)

Apply sample genomic sequence    Enter bisulfite sequences in multi-FASTA format

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. or upload bisulfite sequence file (multi-FASTA format file or zipped archive of sequence files)

Sequence group name (optional):     Apply sample bisulfite sequences    Optional: Enter second bisulfite sequences for statistical analysis (in multi-FASTA format) or upload second bisulfite sequence file for statistical analysis (multi-FASTA format file or zipped archive of sequence files) Sequence group name (optional):     Apply sample bisulfite sequences

Conditions to exclude low quality sequences  (CpH: CpA, CpC, CpT)       Upper limit of unconverted CpHs     Lower limit of percent converted CpHs     Upper limit of alignment mismatches     Lower limit of percent identity    Conversion      C => T conversion (conversion of forward strand of the genomic sequence)    G => A conversion (conversion of reverse strand of the genomic sequence)    Both (search both directions and select the best result)    Strict CpG site check of bisulfite sequence for repetitive sequence analysis:      Exclude identical bisulfite sequences:

Show options Go to Home Page

Upload QUMA restore file (.qma) to restore the analysis

What's New

May 15 2019, Jul 19 2014, Jan 16 2014, Apr 9 2013 Minor modification Oct 25 2012 Minor bug fixed Aug 23 2012 ABI format file (with ".ab1" extension) is now acceptable for bisuflite sequece file May 23 2012 Exclude identical bisulfite sequences option is added (Click above 'Show options' to display) Previous News

Supported browsers

We support the following web browsers; Firefox (Mac/Win) Safari (Mac) Opera (Mac/Win) Internet Explorer(IE) 6.0 and higher (Win)  (IE 7/8 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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				If you have any questions/comments/requests etc., please feel free to contact  :  quma@cdb.riken.jp
				If you link to QUMA web site, please use this URL http://quma.cdb.riken.jp/
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Last updated at Wed May 15 19:00:00 JST 2019