Dear Geneious Team,
A very helpful feature would be to be able to highlight Restriction Endonucleases with impaired cutting by procaryotic(actualy E. coli KI) DNA methylation.
This is quite a hassle in the lab for cloning, especially for our newer lab members.
The info about methylation sensitivity of RE's is on REbase but not easily available.
For an example:
http://rebase.neb.com/cgi-bin/damlist?eXbaI
Find an extensive article here:
https://www.neb.com/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation
If you could just implement the E. coli methylation in some way that would already be helpful.
A possible workaround would be to implement Dam, Dcm & EcoKI as "Enzymes" to search the DNA for. If overlapping occurs one would still have to look if cutting is impaired or not. Not much, but still better than nothing.
I would also be happy to use a Plugin if that's easier.
I mean you don't have to cover all organisms since almost everybody uses the same E. coli strains for cloning.
Best wishes
Lukas
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That's a start - but the trouble with most enzymes is that they are only affected sometimes.
So I might have a sequence with two XbaI sites and one is cutting since there is no overlapping methylation while the other is impaired because of methylation.
That's why it would be helpful to somhow display it at the sequence level.
Thanks for letting them know..
The methylation sensitivity for a given enzyme can be seen in the restriction enzyme advanced options when you choose which enzymes to select:
However this information isn't shown on the actual sequence when a cut site is annotated. I've logged a feature request for this with the developers.
+1 to request this feature.
Lukas - the workaround I'm using, which you may well have found out yourself is to annotate using Search for Motifs (GATC for dam, CCWGG for dcm) which will then create a new track highlighting all the potential methylation sites. Viewing the track alongside the restriction site annotations allows me to quickly spot potential problems.
