Designing primers for multiplex - BLASTing lots of primers (Oct/07/2005 )
Sorry if this has been answered already, but I'm new to this stuff and don't know the proper terms.
I need to design primers for some 40-60 SNPs for use with MALDI.
I need to set up multiplex reactions, as many loci per reaction as I can, to reduce work and costs (I don't have acces to any robotic workstation and money is also a problem).
I already tested many softwares for primer design (Primer3, Oligo, Primer Premier...) and found Primer Premier to be the easiest to work with - I have yet to test FastPCR, SEQtools and PerlPrimer which I have already installed - and I'm also using AutoDimer to test all the multiplexed primers for dimer formation (easier to save the data than Primer Premier).
Now I need to BLAST all my primer sequences and check for inespecific alignments. I think I've figured how to do it for one sequence at a time, but as have some 100+ primers to check, it is not practical.
How can I do a batch search for all the primers at once?
I'm using SEQtools but it's not retrievin any information nor saving the data...
Thanks a lot for your help.
hi you can use ispcr or blat on Genome Browser
they accecpt a tab delimited and fasta format respectively.
I've just discovered (yesterday night) another online software that is very efficient and simple to use.
It BLASTs all the sequences at once and even does in silico PCR to check for inespecific products (although the combinations for in silico PCR must be performed manually).
PUNS, at http://okeylabimac.med.utoronto.ca/PUNS/
cool website, pretty helpful too!