MXfold: the max-margin based RNA folding algorithm
=========================================================================

Requirements
---------------

* C++11 compatible compiler (tested on Apple LLVM version 6.1.0 and GCC version 4.8.1)
* [Vienna RNA package](https://www.tbi.univie.ac.at/RNA/) (>= 2.3)

Install
---------

    export PKG_CONFIG_PATH=/path/to/vienna-rna/lib/pkgconfig:${PKG_CONFIG_PATH}
    mkdir build && cd build
    cmake -DCMAKE_BUILD_TYPE=Release ..
    make

Usage
------

MXfold can take a FASTA formatted RNA sequence as input, then predicts
its secondary structure.

	% mxfold test.fa
	> DS4440
    GGAUGGAUGUCUGAGCGGUUGAAAGAGUCGGUCUUGAAAACCGAAGUAUUGAUAGGAAUACCGGGGGUUCGAAUCCCUCUCCAUCCG
    >structure
    (((((((........(((((..(((.......)))...)))))..(((((......))))).(((((.......)))))))))))).

Web server
----------

A web server is working at http://www.dna.bio.keio.ac.jp/mxfold/.

License
---------

Copyright (c) 2017-2019 Kengo Sato, Manato Akiyama  
Released under the MIT license  
http://opensource.org/licenses/mit-license.php


Acknowledgments
--------------------

MXfold is based on the source code of [CONTRAfold](http://contra.stanford.edu/contrafold/).


References
-------------

* Akiyama, M., Sato, K., Sakakibara, Y.: A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model, _J. Bioinform. Comput. Biol._, 16(6), 1840025 (2018), DOI: [10.1142/S0219720018400255](https://doi.org/10.1142/S0219720018400255).