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

Christian Rohde1, Yingying Zhang1, Richard Reinhardt2 and Albert Jeltsch1*

Author affiliations

1 School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany

2 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany

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Citation and License

BMC Bioinformatics 2010, 11:230  doi:10.1186/1471-2105-11-230

Published: 6 May 2010

Abstract

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/ webcite.