polymerase-tm 0.1.0

Exact reproduction of the NEB Tm Calculator for PCR primer analysis with all NEB polymerases

polymerase-tm

Exact Python reproduction of the NEB Tm Calculator for PCR primer melting temperature (Tm) and annealing temperature (Ta) prediction.

Features

• Exact NEB Tm Calculator reproduction -- algorithm reverse-engineered from the NEB Tm Calculator front-end source; verified against the official tool with 0 degC deviation across all tested sequences.
• 22 NEB polymerase products with their specific buffer salt concentrations and Ta rules (Q5, Phusion, Taq, OneTaq, LongAmp, Vent, Deep Vent, and more).
• DMSO recommendation -- analyses primer hairpins, amplicon GC content, GC-rich hotspots, and template secondary structures.
• CLI tool (polymerase-tm) for quick calculations from the terminal.
• No dependencies for core Tm/Ta calculations. Biopython is optional (only needed for reading GenBank template files in DMSO analysis).

Installation

# From PyPI
pip install polymerase-tm

# With Biopython support (for GenBank template analysis)
pip install polymerase-tm[bio]

# From conda-forge (when available)
mamba install -c conda-forge polymerase-tm

Quick Start

Python API

from polymerase_tm import tm, ta, dmso_recommendation

# Single primer Tm (Q5, 500 nM)
print(tm("ATGTCCCTGCTCTTCTCTCGATGCAA"))          # 72

# Primer pair Ta
result_ta, tm_fwd, tm_rev = ta(
    "ATGTCCCTGCTCTTCTCTCGATGCAA",
    "GTGCCTCCGAGCCAGCACC",
)
print(f"Ta = {result_ta}, Fwd Tm = {tm_fwd}, Rev Tm = {tm_rev}")
# Ta = 72, Fwd Tm = 72, Rev Tm = 75

# Different polymerase
print(tm("ATGTCCCTGCTCTTCTCTCGATGCAA", polymerase="taq"))

# Ta with 3% DMSO
ta_dmso, _, _ = ta("ATGTCCCTGCTCTTCTCTCGATGCAA", "GTGCCTCCGAGCCAGCACC", dmso_pct=3)
print(f"Ta with 3% DMSO = {ta_dmso}")  # 70

# List all available polymerases
from polymerase_tm import list_polymerases
for p in list_polymerases():
    print(f"{p['key']:25s} {p['description']}")

DMSO Analysis

from polymerase_tm import dmso_recommendation, print_dmso_report

report = dmso_recommendation(
    fwd_bind="ATGTCCCTGCTCTTCTCTCGATGCAA",
    rev_bind="GTGCCTCCGAGCCAGCACC",
    template_file="template.gbk",     # optional, requires biopython
)
print_dmso_report(report)

Command Line

# Single primer Tm
polymerase-tm ATGTCCCTGCTCTTCTCTCGATGCAA

# Primer pair Ta
polymerase-tm ATGTCCCTGCTCTTCTCTCGATGCAA GTGCCTCCGAGCCAGCACC

# Different polymerase
polymerase-tm --polymerase taq ATGTCCCTGCTCTTCTCTCGATGCAA GTGCCTCCGAGCCAGCACC

# With DMSO correction
polymerase-tm --dmso 3 ATGTCCCTGCTCTTCTCTCGATGCAA GTGCCTCCGAGCCAGCACC

# List all polymerases
polymerase-tm --list

# DMSO analysis with template
polymerase-tm --dmso-check --template template.gbk ATGTCCCTGCTCTTCTCTCGATGCAA GTGCCTCCGAGCCAGCACC

Algorithm

Component	Method	Reference
Nearest-neighbor Tm	SantaLucia (1998)	PNAS 95:1460-5
Salt correction	Owczarzy et al. (2004)	Biochemistry 43:3537-54
Ta rules	Polymerase-specific	NEB Tm Calculator v1.16
DMSO correction	-0.6 degC per 1%	NEB Tm Calculator v1.16

Buffer Salt Concentrations

Buffer	[Monovalent] (mM)	Used by
Q5	150	Q5, Q5 Hot Start, Q5 Blood Direct
Q5U	170	Q5U Hot Start
Q5 Master Mix	150	Q5 2X Master Mix
Phusion HF / GC	222	Phusion, Phusion Hot Start Flex
Standard Taq	55	Taq, Hot Start Taq, EpiMark
ThermoPol	40	Vent, Deep Vent
OneTaq Std	54	OneTaq (Standard Buffer)
OneTaq GC	80	OneTaq (GC Buffer)
LongAmp	100	LongAmp, LongAmp Hot Start
Crimson Taq	55	Crimson Taq
Hemo KlenTaq	70	Hemo KlenTaq
Multiplex	90	Multiplex PCR Master Mix

Ta Calculation Rules

Polymerase family	Rule	Cap
Q5	min(Tm1, Tm2) + 1	72 degC
Q5U	min(Tm1, Tm2) + 2	72 degC
Phusion	0.93 * min(Tm1, Tm2) + 7.5	72 degC
Taq / OneTaq	min(Tm1, Tm2) - 5	68 degC
LongAmp	min(Tm1, Tm2) - 5	65 degC
Vent / Deep Vent	min(Tm1, Tm2) - 2	72 degC

Disclaimer

This package is not affiliated with New England Biolabs (NEB). The algorithm was reverse-engineered from the publicly available JavaScript source of the NEB Tm Calculator for research and educational purposes. Always verify critical calculations against the official tool.

License

MIT