Dumb question I know, but...
What tool to use?
I'd like to find forward and reverse primers within an approximate distance of each other... I'd like to accept 1 or two mismatches. The genome is ~1 Gbp. I have ~500 forward reverse pairs to find in the genome.
Any hints appreciated :-)
I think you need to be more specific with your question: what are you trying to do? 500 pairs of "primers": are you targeting something in particular or just random? Will these sequences be used for wet lab experiments like PCR or qPCR? Etc.
do you need some random primers or do you know your 500 targets ?
Yes, please be more clear. Do you (1) have 500 forward and reverse 28 bp sequences that you wish to align to the genome sequence? Or (2) want to generate 500 forward/reverse primers using the genome sequence?