Previously we used a very roundabout method to target the probe, by excluding non-wanted regions. The way I did this was marginally wrong though (it did not exclude quite enough space), and so sometimes the probe could miss the actual target.
I've found a simpler primer3 parameter, 'SEQUENCE_INTERNAL_OVERLAP_JUNCTION_LIST,' which will make the probe overlap the target SNP. I don't know if this was available when I first started using primer3-py (some options were not implemented in an earlier version), or I just missed it.
Previously we used a very roundabout method to target the probe, by excluding non-wanted regions. The way I did this was marginally wrong though (it did not exclude quite enough space), and so sometimes the probe could miss the actual target.
I've found a simpler primer3 parameter, 'SEQUENCE_INTERNAL_OVERLAP_JUNCTION_LIST,' which will make the probe overlap the target SNP. I don't know if this was available when I first started using primer3-py (some options were not implemented in an earlier version), or I just missed it.