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        "author": "Gabriele Girelli",
        "author_email": "gabriele.girelli@scilifelab.se",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "oligo-melting v2.0.1.post3\n===\n\nA Python3 package for melting temperature calculation of oligonucleotides hybridization and secondary structures.\n\n#### Features\n\n* Handles DNA:DNA, RNA:RNA and DNA/RNA hybridizations.\n* Corrects for both salt and chemicals.\n* Compatible with UNAfold (OligoArrayAux) output for direct salt and chemicals (denaturants) correction.\n* Produces melting curves for the provided sequence.\n* Input either as single sequence or FASTA file.\n* Slightly faster than BioPython.SeqUtils.MeltingTemp.\n* Provides dG, dS and dH alongside melting temperature.\n\n#### Limitations\n\n* Does not handle mismatches or dangling ends\n* Does not handle ambiguous bases\n\nInstallation\n---\n\nTo **install**, run the following:\n\n```\ngit clone http://github.com/ggirelli/oligo-melting\ncd oligo-melting\nsudo -H pip3 install .\n```\n\nTo **uninstall** run the following from within the repository folder:\n\n```\nsudo -H pip3 uninstall oligo_melting\n```\n\nTo **update**, first uninstall, and then run the following from within the repository folder.\n\n```\ngit pull\nsudo -H pip3 uninstall oligo_melting\nsudo -H pip3 install .\n```\n\nUsage\n---\n\n### From command line\n\n#### Duplexes\n\nThe `melt_duplex` command allows to calculate the melting temperature of a nucleic acid duplex, provided the sequence of one of the two strands.\n\nThe 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].\n\n* Use the `-t` option to specify the **type of nucleic acid duplex**.\n* Use `--fa-mode` to switch between linear melting temperature **formamide-based correction**[7] and linear ΔG formamide-based correction[8].\n* Use `--fa-mvalue` together with `--fa-mode wright` to specify the **m-value** for the formamide-based correction.\n* Provide the path to a **fasta file** instead of a single sequence to calculate the melting temperature of every sequence in the file.\n* Use the `-v` option to trigger the verbose mode, which provides more **details** for every single sequence.\n* Use `-C` for the temperature in **degree Celsius** instead of Kelvin.\n* 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`.\n\n#### Secondary structure\n\nThe `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.\n\n### As a library\n\nImport the package and use the corresponding functions.\n\n```python3\nimport oligo_melting as OligoMelt\n\nseq = \"CAGTCAGTCGATC\"\n\n# Calculate melting temperature for 25uM oligos\n(name, g, h, s, tm, seq) = OligoMelt.Duplex.calc_tm(seq, oligo_conc = 25e-6)\nprint(tm)\n\n# Adjust for 300 mM [Na+]\ntm = OligoMelt.Duplex.adj_ions(tm, 0.3, 0, seq)\nprint(tm)\n```\n\nThe `Duplex` module contains functions for duplex hybridization and melting temperature calculation, while the `SecStr` module contains similar methods for evaluating secundary structure melting temperatures.\n\nReferences\n---\n\n* [1]: Freier et al, PNAS(83), 1986;\n* [2]: Sugimoto et al, Biochemistry(34), 1995.\n* [3]: Allawi & Santalucia, Biochemistry(36), 1997;\n* [4]: SantaLucia, PNAS(95), 1998;\n* [5]: Owczarzy et al, Biochemistry(43), 2004;\n* [6]: Owczarzy et al, Biochemistry(47), 2008;\n* [7]: McConaughy et al, Biochemistry(8), 1969;\n* [8]: Wright et al, Appl. env. microbiol.(80), 2014.\n\nLicense\n---\n\n```\nMIT License\nCopyright (c) 2017 Gabriele Girelli\n```\n\n---\n\nThis project comes from the [potpourri](https://github.com/ggirelli/potpourri) sandbox.  \\\\( \uff9f\u30ee\uff9f)/",
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