GenoScan version v1.0.0
============================

This Perl module is the implementation of the GenoScan software for genome-scale miRNA discovery. It is
composed of a set of Perl pm files accompanied by a C library. The module has been tested to install and run
in Linux Ubuntu and Mac OS X. See the online documentation at CPAN for more detailed information about
how to use GenoScan.

INSTALLATION

To install this module in Ubuntu, navigate to this folder in a
terminal and type the following:

   perl Build.PL
   ./Build
   sudo ./Build install

DEPENDENCIES

This module requires the following Perl modules to be installed:
-Module::Build
-ExtUtils::CBuilder
-XSLoader
-Exporter
-POSIX

In addition, a GNU C compiler is required for module installation.

The following third-party program is also required: RNAfold

RUNNING GENOSCAN

The quickest way to test the algorithm is to use the run_genoscan.pl script in the t/ folder. After the
module is installed, navigate the the t/ folder and type the following:

perl run_genoscan.pl -d fake_genome -o output

For a description of command line arguments, input and output files, please see the CPAN documentation.

SUPPLEMENTARY DATA

The distribution contains the datasets used for benchmarking in [1]. These are located in the datasets
directory. Each dataset has a hairpin version containing only hairpins, and a window version with
200 nt windows containing the hairpins.

COPYRIGHT AND LICENCE

Copyright (C) 2014 by Benjamin Ulfenborg

This module is free to use, modify and redistribute at will.

REFERENCE

[1] Ulfenborg B, Klinga-Levan K, Olsson B (2014) GenoScan: Genomic Scanner for Putative miRNA Precursors.
    Bioinformatics Research and Applications, LNBI 8492, pp. 266-277.