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PMID: 20459626 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

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

BMC bioinformatics ·Vol. 11 ·2010-05-06 ·Pages 230

Rohde C, Zhang Y, Reinhardt R, Jeltsch A

Abstract

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. 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. 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/.

MeSH Terms
Base Sequence Clone Cells DNA/chemistry DNA Methylation Genomics/methods Molecular Sequence Data Repetitive Sequences, Nucleic Acid Sequence Alignment Sequence Analysis, DNA/methods Software Sulfites/chemistry User-Computer Interface
Chemicals
Sulfites DNA hydrogen sulfite
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Rohde Christian
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.
Zhang Yingying
Reinhardt Richard
Jeltsch Albert
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-11-230
Published
2010-05-06
Epub
2010-00-06
Pages
230
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2877691
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2105-11-230 PMC Full Text View journal details
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