I'm looking for a PCR design tool which not only identifies the largest ORF from a DNA sequence, but crucially can design primers for a desired amplicon size/range within that ORF. Preferably allows batch submission of sequences for primer design too. Any help or suggestions would be much appreciated.
Hey Fergal,
Primer3 plus.
I don't know if this does exactly what you want, but there are several settings you can play around with. You might have to identify ORFs using a different program. But, this is a good start.
Adam
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
Deat Fergal primer BLAST operates in the same way as primer 3 but is part of the GenBank NCBI suite thus you can identify genes/ORF (CDs) and then ask primer blast to select primers specifically within this region
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
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