BIOphysics & SOFT Matter Department of Ultrafast Optics and Nanophotonics

Institut de Physique et Chimie des Matériaux de Strasbourg

[No group meeting scheduled]
Background

ThermoFisher has a PCR Calculator, which is basic. This just calculates ~ [1-l x numcycles x u] (l, fragment length; u, error rate), which is nothing else than the probality for a molecule of length l x numcycles to have no errors. Thus, it assumes 100% efficiency and ignores that some molecules are not replicated and contribute to the overall number of molecules without errors.
Here, I use a more rigourous approach (a good article can be found here ). Just enter the parameters below and submit the code (using the Opencpu cloud server; this might takes a few seconds to get the result). Also notice that the calculations are made for 1E3 molecules only.

Enzyme

Length

Cycles




.../...


Adapted from Potapov V, Ong JL PLOS ONE 2017
Enzyme Error Rate Fidelity rel. Taq
Taq 1.5E-4 1
Q5 5.3E-7 280
Phusion 3.9E-6 39
Deep Vent 4.0E-6 44
Pfu 5.1E-6 30
PrimeSTAR 8.4E-6 18
KOD 1.2E-5 12
Kapa HIFI 1.6E-5 9.4
DV Exo- 5.0E-4 0.3