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BISMA specifications

Information


Unique identifier OMICS_00592
Name BISMA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Publication for BISMA

BISMA citations

 (49)
library_books

The DNMT3A R882H mutant displays altered flanking sequence preferences

2018
Nucleic Acids Res
PMCID: 5887309
PMID: 29518238
DOI: 10.1093/nar/gky168

[…] fragment and primers specific for the converted DNA (GTG GGA TTT GGT TTT GTT TTG TAT TTT and GAA TAT TAC TAC TAC CCT CCT CCT TCT CAA TTT AAC) covering 56 CpG sites as described (,) and analyzed with BISMA (,). […]

library_books

Genome wide determination of on target and off target characteristics for RNA guided DNA methylation by dCas9 methyltransferases

2018
GigaScience
PMCID: 5888497
PMID: 29635374
DOI: 10.1093/gigascience/giy011

[…] nd transformed into chemically competent Escherichia coli cells. Cell clones were manually picked, subcultured in 250 uL LB medium overnight, lysed, subjected to Sanger sequencing, and analyzed using BISMA []. […]

library_books

Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy

2018
BMC Genomics
PMCID: 5801776
PMID: 29409445
DOI: 10.1186/s12864-018-4509-0

[…] es), and a total of 31 sequences from corn pools (16 CF sequences and 15 CM sequences) were analyzed to assess the DNA methylation percentage. The CpG sites 1–3, 12, and 13 were not recognized by the BISMA software and were excluded from the analysis. The percentage of DNA methylation was significantly (P = 0.002) higher in fetal LD tissues from hay-fed dams (M + F) with 80.15% methylated CpG site […]

library_books

OCT4 expression mediates partial cardiomyocyte reprogramming of mesenchymal stromal cells

2017
PLoS One
PMCID: 5720736
PMID: 29216265
DOI: 10.1371/journal.pone.0189131

[…] gel-purified with QIAquick Gel Extraction Kit (Quiagen) and then cloned into bacteria by pGEM-T easy cloning (Invitrogen). Sequences of 10–15 bacterial clones per sample examined were analyzed using BISMA software []. Bisulphite conversion efficiency of non-CpG cytosines was higher than 95% for all individual clones for each sample. […]

library_books

Reduced levels of methyltransferase DNMT2 sensitize human fibroblasts to oxidative stress and DNA damage that is accompanied by changes in proliferation related miRNA expression

2017
Redox Biol
PMCID: 5568885
PMID: 28843151
DOI: 10.1016/j.redox.2017.08.012

[…] used for the assessment of the methylation levels in CG context (number of clones with cytosine at particular CpG sites after bisulfite sequence alignment to the unconverted genomic reference) using BISMA software . […]

library_books

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13 gene panel

2017
Clin Epigenetics
PMCID: 5558660
PMID: 28814981
DOI: 10.1186/s13148-017-0386-7

[…] uated in normal donors, which was found very close to 50% as expected: 0.47 ± 0.14 (see Additional file ).An example of the methylation analysis using BISMA (http://services.ibc.uni-stuttgart.de/BDPC/BISMA/manual_unique.php) [] as a web tool is shown in Fig. , representing a comparison for KIF1A among case 1 (OSCC), its normal contralateral mucosa, case 31 (HG-SIL), and a healthy donor. Most OSCC […]

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BISMA institution(s)
School of Engineering and Science, Jacobs University Bremen, Bremen, Germany

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