Question: how to visualize DNA methylation regions in a given genome sequence??
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gravatar for kifayatvet
5 weeks ago by
kifayatvet0
kifayatvet0 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 • 231 views
ADD COMMENTlink modified 5 weeks ago by ATpoint16k • written 5 weeks ago by kifayatvet0
1
gravatar for ATpoint
5 weeks ago by
ATpoint16k
Germany
ATpoint16k 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 5 weeks ago by ATpoint16k
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gravatar for pltbiotech_tkarthi
5 weeks ago by
CIMMYT, Mexico
pltbiotech_tkarthi170 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 5 weeks ago • written 5 weeks ago by pltbiotech_tkarthi170

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

ADD REPLYlink written 5 weeks ago by Devon Ryan89k
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