Link methylation patterns to restriction enzymes

Question

[mschmid]

Do you know of any ressource/way to link methylatoin patterns to enzymes?

Here is what I have exactly:

1. Complete Genome of three diffierent Lactobacillus species
2. Annotation for those Genomes
3. Methylatoin patterns as calculated for PacBio data for the three strains (With PacBios methylation module in SMRT portal)

Now I have some restriction/modification systems and would like to find out which methylation patterns are probably linked to them.

[phco]

Hi mschmid

1) How did you find your RM systems? Are they purely based on annotation? If so, I wouldn't trust them entirely. There are many wrongly assigned types, and others, which may be more degenerate, are indicated as 'hypothetical proteins'. I would suggest you to build hmm profiles for your endonuclease and methyltransferases based on gold standard sequences (for example from REBASE). Then, with these in hand, map your RM systems and solitary MTases.

2) Since your hmm profiles were built on the basis of gold standards for which the target recognition is known, it is straightforward to infer from your hits, the likely recognition motif. I would say that for 99% of the cases this strategy will work.

Have a look at the pipeline published here: https://www.ncbi.nlm.nih.gov/pubmed/25120263 Good luck!