Primer design on assembly

[lorendarith]

Hi,

I would like to sequence a 1kb region from a genome I am currently assembling. My current 800Mb assembly has around 9000 scaffolds and is far from being finished but I have to compare two different individuals to see whether they come from different populations.

So I thought it would be enough to just Sanger sequence a random 1kb part and hope to see a difference between them (unless I hit a really conserved region). I've never constructed primers myself for anything but as far as I've seen most online/offline software works on "short" sequences rather than chromosomes or entire genomes.

How should I go about this and which primer designing software should I use? Would just blasting primers do the job?

Thx!

[boetsie]

Maybe have a look at this one;

http://perlprimer.sourceforge.net/tutorial.html

I don't know about its performance, but I think it can handle whole genomes, at least for bacterial ones.

Regards,
Boetsie

[lorendarith]

Thank you Boetsie, I'll try it out.