BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences

被引：190

作者：

Rohde, Christian ^{[1
]}

Zhang, Yingying ^{[1
]}

Reinhardt, Richard ^{[2
]}

Jeltsch, Albert ^{[1
]}

机构：

[1] Jacobs Univ Bremen, Sch Sci & Engn, D-28725 Bremen, Germany

[2] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

来源：

BMC BIOINFORMATICS | 2010年 / 11卷

关键词：

DNA METHYLATION; CLUSTAL-W; TOOL; SENSITIVITY; EPIGENETICS; CANCER;

D O I：

10.1186/1471-2105-11-230

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Bisulfite sequencing is a popular method to analyze DNA methylation patterns at high resolution. A region of interest is targeted by PCR and about 20-50 subcloned DNA molecules are usually analyzed, to determine the methylation status at single CpG sites and molecule resolution. Results: The BISMA (Bisulfite Sequencing DNA Methylation Analysis) software for analysis of primary bisulfite sequencing data implements sequencing data extraction and enhanced data processing, quality controls, analysis and presentation of the methylation state. It uses an improved strategy for detection of clonal molecules and accurate CpG site detection and it supports for the first time analysis of repetitive sequences. Conclusions: BISMA works highly automated but still provides the user full control over all steps of the analysis. The BISMA software is freely available as an online tool for academic purposes for the analysis of bisulfite sequencing data from both unique and repetitive sequences http://biochem.jacobs-university.de/BDPC/BISMA/.

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