/melt

Standalone nucleotide sequence melt temp calculator for Python

Primary LanguagePythonGNU Affero General Public License v3.0AGPL-3.0

Melt

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A nucleotide sequence melt temp calculator for Python.

Features:

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:

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