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melting

Methods for calculating melting temperatures.

There is currently one public method available:

Examples

>>> calculate_long_seq_tm(seq="GT" * 10, salt_molar_concentration=10.0, percent_formamide=10.0)
78.64999999999999

Functions

calculate_long_seq_tm 

calculate_long_seq_tm(
    seq: str,
    salt_molar_concentration: float = 1.65,
    percent_formamide: float = 15.0,
) -> float

Calculate the melting temperature of an amplicon.

Uses the formula:

Tm = 81.5 + 0.41(%GC) - 675/N + 16.6 x log[Na+] - 0.62(%F)

from:

(Marmur & Doty 1962, J Mol Biol 5: 109-118; Schildkraut & Lifson 1965, Biopolymers 3: 195-208)

with the added chemical (formamide) correction.

Parameters:

Name Type Description Default
seq str

the amplicon sequence

 required
salt_molar_concentration float

the molar concentration of salt

 1.65
percent_formamide float

the percent formamide

 15.0

Returns:

Type Description
float

the predicted melting temperature
Source code in prymer/api/melting.py 
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def calculate_long_seq_tm(
    seq: str, salt_molar_concentration: float = 1.65, percent_formamide: float = 15.0
) -> float:
    """Calculate the melting temperature of an amplicon.

    Uses the formula:

    `Tm = 81.5 + 0.41(%GC) - 675/N + 16.6 x log[Na+] - 0.62(%F)`

    from:

    (Marmur & Doty 1962, J Mol Biol 5: 109-118; Schildkraut & Lifson 1965, Biopolymers 3: 195-208)

    with the added chemical (formamide) correction.

    Args:
        seq: the amplicon sequence
        salt_molar_concentration: the molar concentration of salt
        percent_formamide: the percent formamide

    Returns:
        the predicted melting temperature
    """
    return (
        81.5
        + (16.6 * math.log10(salt_molar_concentration))
        + (41.0 * gc_content(seq))
        - (675.0 / len(seq))
        - (0.62 * percent_formamide)
    )