Restriction Sites Fragments For Gbs/Ddrad

Question

[Bart Ulaszewski]

Hi I'm still a newbie in bioinformatics. I would like to know ( in theory) which enzyme is the best for GBS/ddRAD. My question is how to make a in silico whole plant genome enzyme digestion (e.g. ApeKI, EcoRI etc.) and distribution of fragments? Do you have any tips? Which pipeline/program is the best? Anything that could direct me on the right track... Please help

[Chanz R]

@Devon Ryan can you please explain how to calculate fragment lengths. I am a beginner at python, and I don't find very trivial.

Thanks

[Devon Ryan]

Please post a new question rather than adding one as an answer to a question from almost 5 years ago.

[Chanz R]

Sorry for that, was not my intention. I thought I was on the comment portion.

Here is the new question:

Calculate fragment length from Bio.Restriction Analysis Object

Best!

Answer 1

[Devon Ryan]

It would be simplest to use biopython, possibly using a RestrictionBatch. You then get the locations of all of the cut sites, from which the fragment lengths can be trivially derived.