BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.
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/.
Rohde
Christian
C
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.
Zhang
Yingying
Y
Reinhardt
Richard
R
Jeltsch
Albert
A
D001483:Base Sequence; D002999:Clone Cells; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry*; D014584:User-Computer Interface
D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite
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