search

matdoering / openPrimeR

An R Package for Multiplex PCR Primer Design and Analysis
http://openprimer.mpi-inf.mpg.de
24 stars 6 forks source link

Amplicon size #17

Open Jadelrea opened 10 months ago

Jadelrea commented 10 months ago

Thanks for this nice tool @matdoering

I wonder whether it would be possible to specify the desired amplicon size. In my case, I want to amplify small regions of a bunch of genes (one per gene), but I do not mind the specific positions of those. My rationale is maybe this allows for more flexibility in terms of finding the smallest possible set of primers than if I just input small templates with random regions of the genes I am interested in. On the other hand, I do not know whether this could lead to much higher computational requirements.

matdoering commented 5 months ago

Sure, amplicon size could be implemented as another condition for primer design. Indeed, the only limitation would be computational costs. For large amplicon size ranges this could become prohibitively expensive with respect to runtime.