Metadata-Version: 1.1
Name: melt
Version: 1.0.4
Summary: A nucleotide melt temp calculator
Home-page: https://github.com/eclarke/melt
Author: Erik Clarke
Author-email: ecl@mail.med.upenn.edu
License: GPL 3
Description: Melt
        ------------
        .. image:: https://travis-ci.org/eclarke/melt.svg?branch=master
            :target: https://travis-ci.org/eclarke/melt
        .. image:: https://coveralls.io/repos/eclarke/melt/badge.svg?branch=master&service=github
        	:target: https://coveralls.io/github/eclarke/melt?branch=master
        .. image:: https://badge.fury.io/py/melt.svg
            :target: https://badge.fury.io/py/melt
        
        A nucleotide sequence melt temp calculator for Python.
        
        Features:
        ==========
        
        - Usually within a few tenths of a degree C match to IDT's `OligoAnalyzer <https://www.idtdna.com/calc/analyzer>`_
        - 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 <http://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html>`_ module.
         
        
        Installation
        =============
        
        .. code-block:: bash
        
        	$ pip install melt
        
        Usage
        ======
        
        From the command line:
        
        .. code-block:: bash
        
        	$ Tm ATGCATGC
        	44.4
        	$ Tm --dna 200 --na 50 --mg 3 --dntp 0.8 ATGCATGC
        	26.4
        
        
        As a library:
        
        .. code-block:: Python
        
        	>>> 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 (sbassi@genesdigitales.com)
        - Greg Singer (singerg@tcd.ie)
        - Nicolas Le Novere (lenov@ebi.ac.uk) 
        
        Salt concentration equations adapted from IDT, with work from `Erik Clarke <https://github.com/eclarke>`_, `Sesh Sundararaman <https://github.com/sesh-sas>`_, and `Calvin Morrison <https://github.com/mutantturkey>`_.
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
