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Designing RT-RCR Primers according to other species' homology - Using conserved regions as a guide when mRNA isn't known in your a (Sep/11/2007 )

I work mainly with rabbits. Usually, I try to design primers that have mRNA listed on database from either mouse or rat. However, in the interest of increasing the likelyhood of getting a good primer set, I would like to use conserved regions of both mouse and rat (or human), etc. Before, I would align the sequences in multialin ( and try to use an area with fairly good homology. But, for designing primers I have to use a different program (e.g. Primer3), but this can be tricky and I have to manually search the multialin results to see if the primers suggested are in a homologous region. However, I'm convinced there has to be a more efficient way of doing this. Can someone recommend a program whereby I can enter in my FASTA mRNA sequences, and have that program select primers from the regions of homology automatically? This would be a big help to me, especially if it was an online-based program/tool, like primer3 or multialin. Any suggestions appreciated.


if you know the identity regions between your different species by the alignments you made previously, you could target that region using [ and ]