For the thermodynamic characterization of the primers I'm using: https://pypi.python.org/pypi/primer3-py/0.3.0 I'm considering the problem of dimerization between the primer, using the calcHeterodimer function. This is an example:
res = calcHeterodimer('CCGACCCTATGGGACC', 'TTGGTCCCATAAGGGTCGG')
an object 'thermoresult' is returned:
thermoresult( structure_found=True, tm=39.92795428766294, ds=-370.12644214999796, dh=-127200.0, dg=-12405.28396717814, align_end_1=16, align_end_2=17 )
1) The thermoresult object returns the tm (melting temperature). I do not know how to interpret this temperature value. For instance, if tm = 39.9 °C, it means that a dimer is formed above this temperature? 2) If I have s1 and s2, which are sequences, and then I have align_end_1 and align_end_2, which are indices, and considering 5' as starting point, it means that s1 starts at align_end_1 and s2 starts at align_end_2?
