Skip to main content

A nucleotide melt temp calculator

Project description

https://travis-ci.org/eclarke/melt.svg?branch=master https://coveralls.io/repos/eclarke/melt/badge.svg?branch=master&service=github https://badge.fury.io/py/melt.svg

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
melt-1.0.4-py2.7.egg (8.2 kB) Copy SHA256 hash SHA256 Egg 2.7
melt-1.0.4-py3.5.egg (8.3 kB) Copy SHA256 hash SHA256 Egg 3.5

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page