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B D P C
DNA methylation analysis platform
BISMA
Manual
Example files
Compilation
Clustering
References
Update description
Useful links
Terms of Usage
Contact information
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B
isulfite
S
equencing DNA
M
ethylation
A
nalysis
Analysis of primary bisulfite sequencing DNA methylation data
CpG
Unique sequences
CpG
Repetitive sequences
BISMA software reference: BMC Bioinformatics 2010, 11:230
Reference Sequence
Paste unconverted genomic sequence here, or submit it as text file below. Do not include the primer sequence!
Submit your single sequencing files [abi] or the extracted sequences [text, fasta] either packed in one zip archive or alternatively compiled in one multi fasta file. Vector sequences will be automatically removed.
Please download and inspect the example files.
Sequencing Data
Job Name [optional]
Analysis Parameter
Lower threshold conversion rate %
0
1
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100
Lower threshold sequence identity %
60
61
62
63
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100
Upper threshold of N-sites at cytosine positions %
1
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40
Upper threshold gaps allowed %
1
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10
11
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100
Detection of clonal molecules
BISMA suggested
strict
Alignment
BISMA suggested
Pairwise
Multiple Sequence
PCR-Product
Sort clones by methylation
Sort descending
Sort ascending
No sorting
Methylation color code
Yellow-Blue
Blue-Red
White-Black
Labels for nucleotides
Every 10th nucleotide
Every 20th nucleotide
Every 30th nucleotide
Every 40th nucleotide
Every 50th nucleotide
CpG-site average
Minimum number of data points necessary
2
3
4
5
6
7
8
9
10
11
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17
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30
Scale format
continuous scale
categorized scale
Scale Layout
Yellow-Blue
Blue-Red
Green-Magenta
White-Black
Program written by Christian Rohde - 2009