Hi,
After comparing multiple (2+) DNA sequences, I want to identify ONLY the restriction sites that changed due to the detected polymorphism. I tried several things by hand, but it's WAY too tedious with many sequences etc. Is there any program/ package that could do that for me? I"m using Geneious, Galaxy, and DNAStar (Sequence Builder, among others). The first - I could not find such utility. In the second, the package [Differential Cleavage] is deprecated and I couldn't get it to work. The third only allows by-hand mutation of sequences which will take WAY too long, and error-prone.
Any suggestions will be greatly appreciated, for they will save me PLENTY of computer watching time.
If it is just one polymorphism then set up text string of polyA then 10bases normal sequence polyA then 10bases mutant sequence then polyA
eg aaaaaaaaacatggcccatgaaaaaaaaaaaaaaaaaacatgagcccatgaaaaaaaaaaaa
then go to NEBCUTTER2 at http://nc2.neb.com/NEBcutter2/ at new england biolabs and run the sequence on nebcutter. It will show all the enzyme cut sites and just look for the differences between the 2 proper sequences
Thank you Paul. I ran such simple systems before (PlosOne 2018).
Here, things are more complicated though. I have 4 LONG sequences (100K+), with way more than just single variation within.
Sorry Marcin Nowicki I overlooked that you wanted an automated method for all sequences. The gene Codes software Sequencher will let you cut contigs but is expensive so if this is a one off project you could get the demo version which will time expire and does not allow saving or printing but will give you an answer. Hopefully someone will know a free software option
I have only one thing to say:
Gotta LOVE Geneious. Thay are absolutely worth the money one pays for their services.
- Badges
- Science method