pydna.tm

This module provide functions for melting temperature calculations.

pydna.tm.tm_default(seq, check=True, strict=True, c_seq=None, shift=0, nn_table=_mt.DNA_NN4, tmm_table=None, imm_table=None, de_table=None, dnac1=500 / 2, dnac2=500 / 2, selfcomp=False, Na=40, K=0, Tris=75.0, Mg=1.5, dNTPs=0.8, saltcorr=7, func=_mt.Tm_NN)

pydna.tm.tm_dbd(seq, check=True, strict=True, c_seq=None, shift=0, nn_table=_mt.DNA_NN3, tmm_table=None, imm_table=None, de_table=None, dnac1=250, dnac2=250, selfcomp=False, Na=50, K=0, Tris=0, Mg=1.5, dNTPs=0.8, saltcorr=1, func=_mt.Tm_NN)

pydna.tm.tm_product(seq: str, K=0.050)

Tm calculation for the amplicon.

according to:

Rychlik, Spencer, and Rhoads, 1990, Optimization of the anneal ing temperature for DNA amplification in vitro http://www.ncbi.nlm.nih.gov/pubmed/2243783

pydna.tm.ta_default(fp: str, rp: str, seq: str, tm=tm_default, tm_product=tm_product)

Ta calculation.

according to:

Rychlik, Spencer, and Rhoads, 1990, Optimization of the anneal ing temperature for DNA amplification in vitro http://www.ncbi.nlm.nih.gov/pubmed/2243783

The formula described uses the length and GC content of the product and salt concentration (monovalent cations)

pydna.tm.ta_dbd(fp, rp, seq, tm=tm_dbd, tm_product=None)

pydna.tm.program(amplicon, tm=tm_default, ta=ta_default)

Returns a string containing a text representation of a suggested PCR program using Taq or similar polymerase.

|95°C|95°C               |    |tmf:59.5
|____|_____          72°C|72°C|tmr:59.7
|3min|30s  \ 59.1°C _____|____|60s/kb
|    |      \______/ 0:32|5min|GC 51%
|    |       30s         |    |1051bp

pydna.tm.taq_program(amplicon, tm=tm_default, ta=ta_default)

Returns a string containing a text representation of a suggested PCR program using Taq or similar polymerase.

|95°C|95°C               |    |tmf:59.5
|____|_____          72°C|72°C|tmr:59.7
|3min|30s  \ 59.1°C _____|____|60s/kb
|    |      \______/ 0:32|5min|GC 51%
|    |       30s         |    |1051bp

pydna.tm.dbd_program(amplicon, tm=tm_dbd, ta=ta_dbd)

Text representation of a suggested PCR program.

Using a polymerase with a DNA binding domain such as Pfu-Sso7d.

|98°C|98°C               |    |tmf:53.8
|____|_____          72°C|72°C|tmr:54.8
|30s |10s  \ 57.0°C _____|____|15s/kb
|    |      \______/ 0:15|5min|GC 51%
|    |       10s         |    |1051bp

|98°C|98°C      |    |tmf:82.5
|____|____      |    |tmr:84.4
|30s |10s \ 72°C|72°C|15s/kb
|    |     \____|____|GC 52%
|    |      3:45|5min|15058bp

pydna.tm.pfu_sso7d_program(amplicon, tm=tm_dbd, ta=ta_dbd)

Text representation of a suggested PCR program.

Using a polymerase with a DNA binding domain such as Pfu-Sso7d.

|98°C|98°C               |    |tmf:53.8
|____|_____          72°C|72°C|tmr:54.8
|30s |10s  \ 57.0°C _____|____|15s/kb
|    |      \______/ 0:15|5min|GC 51%
|    |       10s         |    |1051bp

|98°C|98°C      |    |tmf:82.5
|____|____      |    |tmr:84.4
|30s |10s \ 72°C|72°C|15s/kb
|    |     \____|____|GC 52%
|    |      3:45|5min|15058bp

pydna.tm.Q5(primer: str, *args, **kwargs)

For Q5 Ta they take the lower of the two Tms and add 1C (up to 72C). For Phusion they take the lower of the two and add 3C (up to 72C).

pydna.tm.tmbresluc(primer: str, *args, primerc=500.0, saltc=50, **kwargs)

Returns the tm for a primer using a formula adapted to polymerases with a DNA binding domain, such as the Phusion polymerase.

Parameters:

• primer (string) – primer sequence 5’-3’

• primerc (float) – primer concentration in nM), set to 500.0 nm by default.

• saltc (float, optional) – Monovalent cation concentration in mM, set to 50.0 mM by default.

• thermodynamics (bool, optional) – prints details of the thermodynamic data to stdout. For debugging only.

Returns:

tm – the tm of the primer

Return type:

float

pydna.tm.tm_neb(primer, conc=0.5, prodcode='q5-0')