Software to in silico test restriction enzymes for GBS sequencing and similar approaches

Question

[Denis]

Hi! We are planning some GBS sequencing experiment. We have the whole genome sequence of organism of interest. But we'd like to test in silico numerous restriction enzymes to choose the best one for our experiment. I wondering, is there any ready program to do that? Particularly, count number of restriction sites in the genome for one or two different enzymes, make distribution of restriction fragment lengths etc. Thanks!

Answer 1

[h.mon]

Apparently, there are several, see these threads:

Q: In Silico Genome Digestion ?

Q: Restriction Sites Fragments For Gbs/Ddrad

Q: how to find the total number of recognition sequence of a restriction enzyme in total human genome ?

Also, see these papers:

https://www.ncbi.nlm.nih.gov/pubmed/27288885

https://www.ncbi.nlm.nih.gov/pubmed/27071032

[Denis]

I've tested ddRADseqTools (the first link from the answer above) and found its very handy for my purposes.