Question: how to visualize DNA methylation regions in a given genome sequence??
1
gravatar for kifayatvet
11 months ago by
kifayatvet10
kifayatvet10 wrote:

Hi

I'm sorry for the basic question but I am confused which bioinformatics tool should I use to locate DNA methylation regions in a given short sequence of the genome. I would really appreciate some clarification. thanks in advance.

sequencing snp alignment • 422 views
ADD COMMENTlink modified 11 months ago by ATpoint29k • written 11 months ago by kifayatvet10
1
gravatar for ATpoint
11 months ago by
ATpoint29k
Germany
ATpoint29k wrote:

In mammalian genomes, DNA methylation typically occurs at CG-dinucleotides (CpG sites). If a CpG site (or any larger aggregation of CpGs like CpG islands or floats) are indeed methylated needs to be determined by experiment, e.g. via Sanger sequencing after bisulfite treatment (lowest thoroughput method) or NGS-based assays like Reduced representation bisulfite sequencing (RRBS) or whole-genome-bisulfite sequencing.

ADD COMMENTlink written 11 months ago by ATpoint29k
0
gravatar for pltbiotech_tkarthi
11 months ago by
CIMMYT, Mexico
pltbiotech_tkarthi180 wrote:

CpG islands are the most preferable sites of DNA methylation. So you can predict CpG islands using EMBOSS server https://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/ or other servers and you could interpret the methylation preferable sites.

ADD COMMENTlink modified 11 months ago • written 11 months ago by pltbiotech_tkarthi180

It's unclear how this would assist in any way with looking at DNA methylation.

ADD REPLYlink written 11 months ago by Devon Ryan94k
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