programme that can take an output from contiguator/ABACAS and design primers

Question

[bobo]

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

[Devon Ryan]

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.

[bobo]

thanks, I meant not a command line program

[Fabio Marroni]

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.

[bobo]

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).