Looking for software that permutes codons to find new restriction sites - (Aug/02/2014 )

Hello forum,

I need your help again. I'm looking for a software / online tool that is able to look through a certain sequence of cDNA and can find "new" restriction sites by changing a single codon so that the initial amino acid is not changed.

I mean it like this:

Starting sequence: GTTGACATGCGAATGCG

Software will suggest: GTCGACATGCGAATGCG

GTT encodes for valine, changing GTT to GTC does not alter the amino acid sequence but gives rise to a SalI restriction site.

I've looked throughout the internet, downloaded a lot of "cloning software" but I wasn't able to find any software / tool that can do this. So if anyone of you knows something that works well (and is free of charge) I'd be very thankful for your input.

Best regards!

-2xzwei-

Use Snapgene (http://www.snapgene.com/). One month trial is free. It's the perfect solution for your problem.

-Rajpoot-

Use Snapgene (http://www.snapgene.com/). One month trial is free. It's the perfect solution for your problem.

-Rajpoot-

Thanks. So I downloaded SnapGene but where can I find this function? Didn't find anything to automatically mutate the sequence in favor of generating new cutting sites... Could you please explain how to proceed?

-2xzwei-

Hi, maybe you can try the WatCut site: http://watcut.uwaterloo.ca/template.php?act=silent_new

-macrox-