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. 2008 Jul 1;36(Web Server issue):W170-5.
doi: 10.1093/nar/gkn294. Epub 2008 May 16.

QUMA: quantification tool for methylation analysis

Yuichi Kumaki  1 , Masaaki Oda, Masaki Okano
Affiliations

QUMA: quantification tool for methylation analysis

Yuichi Kumaki et al. Nucleic Acids Res. .

Abstract

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/.

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Figures

Figure 1.
Figure 1.
Flow and output of the QUMA web server. After data submission, an analytical results page is displayed. Methylation status data for each CpG site, a summary of the sequence alignment of the bisulfite sequences, and the methylation pattern of each sequence are shown on this page. The alignment of the genomic sequence with each bisulfite sequence can be shown in a different window. The analysis results data (CSV format, which can be opened from Excel or other spread-sheet software), alignment data (text format), several types of methylation status figures and methylation pattern figures (PNG format) can be downloaded.
Figure 2.
Figure 2.
The home page and input data formats of the QUMA web server. QUMA needs two types of input files: a PCR target genomic sequence and bisulfite sequences. Acceptable file formats are plain sequence, FASTA or GenBank format for the genomic sequence, and a multi-FASTA format or a zipped archive of sequence files for bisulfite sequences. Optional fields can be seen from the ‘Show options’ link.
Figure 3.
Figure 3.
An example of statistical analysis output at the QUMA web server. In the statistical data section (magenta rectangle), the position of CpG sites, methylation status of each CpG site, and statistical significance (P-values) of differences between two bisulfite sequence groups are shown. A diagram representing the comparative methylation status can be displayed in several different formats.
See this image and copyright information in PMC

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