melt 1.0.4

A nucleotide melt temp calculator

A nucleotide sequence melt temp calculator for Python.

Features:

• Usually within a few tenths of a degree C match to IDT’s OligoAnalyzer

• Mono- and divalent cation corrections (from https://www.idtdna.com/Calc/Analyzer/Home/Definitions#MeltTemp)

• Accurate nucleotide pair coefficents from Allawi and SantaLucia (1997)

Limitations:

• Does not handle mismatches or dangling ends

• Does not handle ambiguous bases

• Does not handle RNA or DNA/RNA hybridization

If you need these features, use BioPython’s MeltingTemp module.

Installation

$ pip install melt

Usage

From the command line:

$ Tm ATGCATGC
44.4
$ Tm --dna 200 --na 50 --mg 3 --dntp 0.8 ATGCATGC
26.4

As a library:

>>> import melting
>>> melting.temp("ATGCATGC")
44.387081560668946
>>> melting.temp("ATGCATGC", DNA_c=200, Na_c=50, Mg_c=3, dNTPs_c=0.8)
26.438734864285152

Acknowledgements

This code is largely built on existing code from:

• Sebastian Bassi ([e-mail])

• Greg Singer ([e-mail])

• Nicolas Le Novere ([e-mail])

Salt concentration equations adapted from IDT, with work from Erik Clarke, Sesh Sundararaman, and Calvin Morrison.