How to design degenerative primer in R?
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3.3 years ago
arpankbasak ▴ 10

I'm struggling to design a degenerative primer in R, I have 8 sets 585 aa seq, for which I have to generate degenerative primers, I have used DECIPHER pipeline for MSA and phylogeny.

R PCR primer • 1.6k views
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I have 8 sets 585 aa seq

Can you be a bit more specific here?

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To be specific, I have list of 8 peptides having a length of ~585 aa. I would like to design a degenerative primer. I'm using R interface. I have to design the Dgen-primers for these 8 distinct peptides, can I do that in R..?

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Which DECIPHER are you talking about?

http://www2.decipher.codes/DesignPrimers.html

Or

https://decipher.sanger.ac.uk/

Assuming it is the first one, can't you use the server to design the primers? Otherwise, as WouterDeCoster indicated, you have to provide more information - such as commands used so far and which command failed, with its error message - in order for us to help.

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I meant DECIPHER.codes by E. Wright. With this package I have successfully designed fwd and rev primers (barcoded) but I havent tried degen-primers, can it be done..? I couldn't find the option for degen-primer.

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3.2 years ago
Tm ★ 1.0k

You can try using hyden, iCODEHOP or genefisher2 . For more options you can check out this post of research gate.

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3.2 years ago
Joe 19k

Why R? This isn’t really its forté.

<10 seconds on google finds a python package that will do just this by the looks of it:

https://pypi.org/project/primer_designer/

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Thanks for the suggestion, this one did the trick. AMAZING!

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