I'm looking at the sequence of a flavivirus virus genome (mRNA). Kindly see the link MH900227.1. How can I identify the Guanine nucleotide that is methylated in the capping process?
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“How can I identify the Guanine nucleotide that is methylated in the capping process?”
Not from the genome sequence MH900227.1 mentioned in the question. It is the sequence of the genomic RNA (given as DNA), it starts with an A and even the full Genbank entry lacks any annotation of whether there is a separate capped mRNA and, if so, where it starts.
To answer your question you will have to search the literature. There is a 2018 review by Göertz et al. entitled Functional RNA during Zika virus infection which should have (or lead to) the answer. It does appear from Figure 1 of that review that Zika virus polyprotein mRNA is capped, although the position is not immediately apparent just skimming the paper. Some hours of work and access to a university library is probably required to track it down.
Why do you think the methylated G is present in these sequences?
I have two reasons for thinking your question isn't answerable.
As I said in my comment, based on BLAST results I don't think your sequence is complete — it appears to be missing the 5' end.
If the 5' end is missing then the end that gets capped is missing.
The 5' cap gets added post-transcriptionally and has a linkage (5′–5′ triphosphate) that prevents it from being sequenced.
That means that sequencing reaction don't see the G that gets methylated in the 5' cap.
This is why I suggest that you make sure you understand the capping process.