HELP, primer design problem in gap closure

[f0415007]

hey guys, i'm newbie here.

i got a question in primer design.

now i've got 100 contigs and starting gap closure using PCR method. i've no idea how to design primer between contigs. using Primer Premier X.0 with ref? is there any software that can import two upstream/downstream contigs to design primer?


and how to avoid repeat region? (blast to ref after primer designing?)


any help would be appreciated. thx

[damiankao]

I would try to align your contigs to the closest related species and try to use that to inform your primer design.