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openscilab / opr

OPR: Optimized Primer
MIT License
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Basic Melting Temperature #1

Closed AHReccese closed 10 hours ago

AHReccese commented 6 months ago

Description

http://biotools.nubic.northwestern.edu/OligoCalc.html

Steps/Code to Reproduce

Expected Behavior

Actual Behavior

Operating System

Python Version

OPR Version (Use : opr.__version__)

sepandhaghighi commented 1 month ago

Reference:

  1. Marmur, J. and Doty, P. 1962 Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol.5109–118

  2. Alejandro Panjkovich, Francisco Melo, Comparison of different melting temperature calculation methods for short DNA sequences, Bioinformatics, Volume 21, Issue 6, March 2005, Pages 711–722, https://doi.org/10.1093/bioinformatics/bti066

Formula:

$${T}_{m}=64.9+41.0\times \left(\frac{y\hbox{ G }+z\hbox{ C }-16.4}{w\hbox{ A }+x\hbox{ T }+y\hbox{ G }+z\hbox{ C }}\right)$$

sepandhaghighi commented 1 month ago

@AHReccese Feel free to begin this task.