Question: How to design degenerative primer in R?
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gravatar for arpankbasak
18 months ago by
arpankbasak10
arpankbasak10 wrote:

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.

pcr primer R • 912 views
ADD COMMENTlink modified 18 months ago by Joe16k • written 18 months ago by arpankbasak10

I have 8 sets 585 aa seq

Can you be a bit more specific here?

ADD REPLYlink written 18 months ago by WouterDeCoster42k

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..?

ADD REPLYlink written 18 months ago by arpankbasak10

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.

ADD REPLYlink modified 18 months ago • written 18 months ago by h.mon29k

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.

ADD REPLYlink written 18 months ago by arpankbasak10
0
gravatar for toralmanvar
18 months ago by
toralmanvar830
toralmanvar830 wrote:

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

ADD COMMENTlink modified 18 months ago • written 18 months ago by toralmanvar830
0
gravatar for Joe
18 months ago by
Joe16k
United Kingdom
Joe16k wrote:

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/

ADD COMMENTlink written 18 months ago by Joe16k

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

ADD REPLYlink written 16 months ago by arpankbasak10

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 16 months ago by WouterDeCoster42k
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