Metadata-Version: 2.1
Name: oligo_melting
Version: 2.0.1.post5
Summary: A Python3 package for melting temperature calculation of
		oligonucleotides hybridization and secondary structures.
Home-page: https://github.com/ggirelli/oligo-melting
Author: Gabriele Girelli
Author-email: gabriele.girelli@scilifelab.se
License: MIT
Description: oligo-melting v2.0.1.post5
        ===
        
        A Python3 package for melting temperature calculation of oligonucleotides hybridization and secondary structures.
        
        #### Features
        
        * Handles DNA:DNA, RNA:RNA and DNA/RNA hybridizations.
        * Corrects for both salt and chemicals.
        * Compatible with UNAfold (OligoArrayAux) output for direct salt and chemicals (denaturants) correction.
        * Produces melting curves for the provided sequence.
        * Input either as single sequence or FASTA file.
        * Slightly faster than BioPython.SeqUtils.MeltingTemp.
        * Provides dG, dS and dH alongside melting temperature.
        
        #### Limitations
        
        * Does not handle mismatches or dangling ends
        * Does not handle ambiguous bases
        
        Installation
        ---
        
        To **install**, run the following:
        
        ```
        git clone http://github.com/ggirelli/oligo-melting
        cd oligo-melting
        sudo -H pip3 install .
        ```
        
        To **uninstall** run the following from within the repository folder:
        
        ```
        sudo -H pip3 uninstall oligo_melting
        ```
        
        To **update**, first uninstall, and then run the following from within the repository folder.
        
        ```
        git pull
        sudo -H pip3 uninstall oligo_melting
        sudo -H pip3 install .
        ```
        
        Usage
        ---
        
        ### From command line
        
        #### Duplexes
        
        The `melt_duplex` command allows to calculate the melting temperature of a nucleic acid duplex, provided the sequence of one of the two strands.
        
        The hybridization delta free energy calculation is based on the N-N thermodynamic values in literature and is available for DNA:DNA[3], RNA:RNA[1] and DNA:RNA[2] duplexes. The melting temperature calculation is based on Santalucia, 1998[4]. Sodium and cagnesium concentration correction is based on the work of Owczarzy et al[5][6]. Formamide correction can be performed based on two different published models[7][8].
        
        * Use the `-t` option to specify the **type of nucleic acid duplex**.
        * Use `--fa-mode` to switch between linear melting temperature **formamide-based correction**[7] and linear &Delta;G formamide-based correction[8].
        * Use `--fa-mvalue` together with `--fa-mode wright` to specify the **m-value** for the formamide-based correction.
        * Provide the path to a **fasta file** instead of a single sequence to calculate the melting temperature of every sequence in the file.
        * Use the `-v` option to trigger the verbose mode, which provides more **details** for every single sequence.
        * Use `-C` for the temperature in **degree Celsius** instead of Kelvin.
        * Use `--out-curve` to specify a file where to save estimated single-sequence **melting curves** with temperature range and step around the melting temperature as defined with `--t-curve`.
        
        #### Secondary structure
        
        The `melt_secstr` script allows to correct the melting temperature of a nucleic acid secondary structure, previously calculated with OligoArrayAux, and to produce the corresponding melting curves.
        
        ### As a library
        
        Import the package and use the corresponding functions.
        
        ```python3
        import oligo_melting as OligoMelt
        
        seq = "CAGTCAGTCGATC"
        
        # Calculate melting temperature for 25uM oligos
        (name, g, h, s, tm, seq) = OligoMelt.Duplex.calc_tm(seq, oligo_conc = 25e-6)
        print(tm)
        
        # Adjust for 300 mM [Na+]
        tm = OligoMelt.Duplex.adj_ions(tm, 0.3, 0, seq)
        print(tm)
        ```
        
        The `Duplex` module contains functions for duplex hybridization and melting temperature calculation, while the `SecStr` module contains similar methods for evaluating secundary structure melting temperatures.
        
        References
        ---
        
        * [1]: Freier et al, PNAS(83), 1986;
        * [2]: Sugimoto et al, Biochemistry(34), 1995.
        * [3]: Allawi & Santalucia, Biochemistry(36), 1997;
        * [4]: SantaLucia, PNAS(95), 1998;
        * [5]: Owczarzy et al, Biochemistry(43), 2004;
        * [6]: Owczarzy et al, Biochemistry(47), 2008;
        * [7]: McConaughy et al, Biochemistry(8), 1969;
        * [8]: Wright et al, Appl. env. microbiol.(80), 2014.
        
        License
        ---
        
        ```
        MIT License
        Copyright (c) 2017 Gabriele Girelli
        ```
        
        ---
        
        This project comes from the [potpourri](https://github.com/ggirelli/potpourri) sandbox.  \\( ﾟヮﾟ)/
Keywords: DNA chemistry melting temperature modeling RNA salt denaturant
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Description-Content-Type: text/markdown
