jcaucb
commented
2 years ago In the 18bp version of PCR simulator, it should check that the 3' ends of the oligos can anneal to themselves or to the other primer by exact match over the last 6 bp. If there is a match, that algorithm should throw an exception and relay onto the more mechanistic algorithm.
The mechanistic PCR simulator should do an initial test by alignment and calculation of Tm to see if there are primer dimers above 50 degC or so. If there is such potential, it should throw an Exception.
During simulation of PCR, it should check each primer with itself and with the other for formation of >55degC dimers. If such exist but do not include the last 6 bp of the 3' end, then a warning is given. If the 3' 6bp is included, it throws an IllegalArgumentException.
This applies only when the size of templates input is >0. Otherwise it is an overlap extension (Klenow) and a primer dimer is exactly what should happen.