title: BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.
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/.
authors.affiliation: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Rohde
authors.forename: Yingying
authors.initials: Y
authors.lastname: Zhang
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Albert
authors.initials: A
authors.lastname: Jeltsch
mesh_terms: 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
chemical_list: D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Nature. 2004 May 27;429(6990):457-63
references.pmid: 15164071
references.citation: Nucleic Acids Res. 2008 Mar;36(5):e34
references.pmid: 18296484
references.citation: Semin Cancer Biol. 2004 Dec;14(6):427-32
references.pmid: 15489135
references.citation: Genomics. 2007 Jun;89(6):687-96
references.pmid: 17418524
references.citation: Nature. 1994 Oct 27;371(6500):752
references.pmid: 7935834
references.citation: Cell Mol Life Sci. 2004 Oct;61(19-20):2571-87
references.pmid: 15526163
references.citation: Cell. 2007 Feb 23;128(4):669-81
references.pmid: 17320505
references.citation: PLoS Genet. 2009 Mar;5(3):e1000438
references.pmid: 19325872
references.citation: Plant J. 2007 Aug;51(3):526-36
references.pmid: 17559516
references.citation: EMBO J. 1993 Mar;12(3):1141-51
references.pmid: 8384552
references.citation: Nucleic Acids Res. 2004 Feb 18;32(3):e38
references.pmid: 14973332
references.citation: Cell. 2007 Feb 23;128(4):693-705
references.pmid: 17320507
references.citation: Genome Res. 2010 Mar;20(3):320-31
references.pmid: 20133333
references.citation: Biotechniques. 2009 Sep;47(3):781-3
references.pmid: 19852764
references.citation: BMC Bioinformatics. 2008 Sep 11;9:371
references.pmid: 18786255
references.citation: Methods Mol Biol. 2009;507:177-87
references.pmid: 18987815
references.citation: PLoS One. 2007 May 02;2(5):e399
references.pmid: 17476321
references.citation: Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827-31
references.pmid: 1542678
references.citation: Mol Cell Biol. 1993 Aug;13(8):4523-30
references.pmid: 8336699
references.citation: Trends Biochem Sci. 2006 Feb;31(2):89-97
references.pmid: 16403636
references.citation: Nature. 2009 Nov 19;462(7271):315-22
references.pmid: 19829295
references.citation: Genomics. 1998 Dec 15;54(3):379-86
references.pmid: 9878240
references.citation: Development. 2004 Mar;131(5):975-82
references.pmid: 14973270
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Genome Biol. 2009;10(12):R138
references.pmid: 19958531
references.citation: Nucleic Acids Res. 1994 Aug 11;22(15):2990-7
references.pmid: 8065911
references.citation: Bioinformatics. 2005 Nov 1;21(21):4067-8
references.pmid: 16141249
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W170-5
references.pmid: 18487274