GenoScan version v1.0.3 ============================ 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 To run GenoScan in classify and benchmark modes (see documentation), R is needed 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 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.