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Map Methylated Sites in a Bacterial Genome
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Reference GBK file
Annotated nucleotide sequences and their protein translations in GenBank flat file format.
GFF file
Methylated sites detected during sequencing in General feature format.
▶ Coverage Plot
The sequencing depth of individual nucleotides vs their NucMod calling scores. Set custom plotting options here:
Plot name.
Cut-off score: Set a cut-off number for NucMod calling score (default = off).
Methylation type: Enter methylation types (m6A,m4C). Both types are shown by default.
Modified nucleotides: Enter a comma separated list of nucleotides (A,C,G,T). This option is off by default.
Size: Set height and width of plot (auto=0).
Plot name
Cut-off score
Methylation type
m6A, m4C
m6A
m4C
Modified nucleotides
Width
Height
Motif Options
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Motif (e.g., "GATC")
A specific nucleotide sequence recognised by methyltransferases. See "Help & Info" for more advanced combinations.
Modified base locations
Specify the modified base locations on the forward/reverse strands of the motif. Each position is separated by a comma, and denoted by a number starting from 1.
For example, if your hypothetical motif is GATC and is modified at A and C, then you would enter: 2,4
Forward Strand
Reverse Strand
Show methylated motifs?
Yes
No
Searching mode
Sites: report any methylated nucleotide found in a given motif.
Motifs: report methylated nucleotides only if all are found in a given motif.
Sites
Motifs
▶ Advanced Parameters
Masked regions
Text file containing genome regions to be ignored.
Allow context mismatches?
The maximum number of methylation site to reference sequence mismatches allowed (default = 2).
Yes
No
Context mismatches
Cut-off score
The likelihood that a given nucleotide is methylated (default = unset). For example, a cut-off of 21 equates to p = 0.01.
Promoter sequence length
The length of the upstream promoter sequence (default = 75).
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