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Looking for software that permutes codons to find new restriction sites


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4 replies to this topic

#1 2xzwei

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Posted 02 August 2014 - 02:39 PM

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!

 



#2 Rajpoot

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Posted 03 August 2014 - 04:55 AM

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



#3 Rajpoot

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Posted 03 August 2014 - 04:59 AM

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



#4 2xzwei

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Posted 03 August 2014 - 06:14 AM

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?


Edited by 2xzwei, 03 August 2014 - 06:31 AM.


#5 macrox

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Posted 18 August 2014 - 11:28 PM

Hi, maybe you can try the WatCut site: http://watcut.uwater...?act=silent_new






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