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cultivarium / MicrobeMod

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
MIT License
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Matching prodigal call with methylation location #17

Closed Ge0rges closed 2 months ago

Ge0rges commented 5 months ago

Hello,

It would be an interesting feature if the tool could use the prodigal output and methylation location to tell us, for example, if the promoter region is methylated, or if the methylation location is coding or non coding.

I think this would be specifically interesting in the analysis of differentially methylated regions (instead of consistently methylated motifs) where DNA methylation may play a role in gene expression. This could also be the place to link with methyltransferases that are found in annotate_rm but not associated with an rm system.

alexcritschristoph commented 5 months ago

I do think that would be cool. Because our focus is mostly on RM and not roles for methylation in gene regulation, I don't plan to add this in the near term, so for the time being people will have to parse that result from the _sites table and their prodigal gff and analyze in the way they see fit.