Annealing temperature by polymerase
Annealing temperature and a full cycling program for a primer PAIR, under the rule the polymerase's own vendor publishes — which is not one rule, and is only defined against the vendor's own Tm. For NEB products the Tm is computed exactly as NEB's Tm calculator computes it (SantaLucia 1998 nearest-neighbor with NEB's salt correction, at that product's own buffer and primer concentration — the same primer's Tm moves ~10 °C between NEB buffers) and NEB's calculator rule is applied to it: Q5 at Tm + 1, Phusion at 0.93 × Tm + 7.5 (both ABOVE the Tm), Taq/OneTaq/LongAmp at Tm − 5, Vent/Deep Vent at Tm − 2 above 20 nt, with NEB's ceilings. Toyobo KOD One is Tm − 5 at the salt and oligo concentration its manual names, Takara PrimeSTAR Max a FIXED 55 °C the primer Tm plays no part in (its own 2(A+T)+4(G+C)−5 sets only the annealing time), and a generic Taq/Pfu row applies the Tm − 3 to − 5 rule of thumb to a default-condition nearest-neighbor Tm. Returns denaturation/annealing/extension steps, cycle count, magnesium guidance, the Tm basis and vendor document behind each figure, and the same primers under every other polymerase in the table for comparison.
Request
- Base URL: https://seqbench.com/api/v1
- URL: https://seqbench.com/api/v1/annealing_temperature
- Auth: none required
Request body
Response
Tool ran successfully.
Example response
{
"provenance": {
"apiVersion": "1.1.0"
}
}Changes
No recorded changes to this operation across all 1 revision of this API.