Question: programme that can take an output from contiguator/ABACAS and design primers
0
gravatar for b.lehri118
5.1 years ago by
b.lehri1180
United Kingdom
b.lehri1180 wrote:

Hi all,

I have a scaffold-ed sequence (scaffold-ed using contiguator). I've tried ABACAS and contiguator to design primers neither seem to produce any primer output. Since both seem to be wrappers around primer3, I think the problem has to do with primer3. Could anyone suggest a way to design primers for a scaffolded sequence (I have 32 gaps that need filling), preferably not a command line program.

Thanks

contiguator abacas primer3 primer • 1.5k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 5.1 years ago by b.lehri1180
1

I took the liberty of editing your question to be somewhat more coherent English (though the title could still use some work). The last sentence, however, was ambiguous. I took "none of command line program" to mean "not a command line program", though perhaps you meant the exact opposite. If so, please either reply or, better yet, simply update your question.

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Devon Ryan90k

thanks, i meant not a command line program

ADD REPLYlink written 5.1 years ago by b.lehri1180

what's the exact problem? Did you use the primer3 website for designing primers and you got no results? I never had problems with primer3 (web version or command line). Maybe you can paste a short example of a small region in which you want to design primers and see if someone can help.

ADD REPLYlink written 5.1 years ago by Fabio Marroni2.2k

sorry i was not very attentive when i wrote the title/question .

I basically want to know whether there are any programmes that can take an output from contiguator/ABACAS and design primers for my sequence.

ABACAS/contiguator orientate and align contigs to a reference but they don’t seem to produce primers for filling in gaps within my sequence. As both are based on primer3 I assume the problem resides within that area.

I have used projector2 (another tool for aligning/orientating contigs to a reference). The programme produces primers for filling in gaps. But I don’t trust the way it orientates/aligns contigs to a reference (I trust contiguator more).

 

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by b.lehri1180
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