Question: Software to in silico test restriction enzymes for GBS sequencing and similar approaches
1
gravatar for Denis
2.1 years ago by
Denis110
Denis110 wrote:

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!

sequencing snp next-gen genome • 1.4k views
ADD COMMENTlink modified 2.1 years ago by h.mon27k • written 2.1 years ago by Denis110
2
gravatar for h.mon
2.1 years ago by
h.mon27k
Brazil
h.mon27k wrote:

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

ADD COMMENTlink written 2.1 years ago by h.mon27k

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

ADD REPLYlink written 2.1 years ago by Denis110
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