GO-TermFinder version 0.21 ========================== This set of modules can be have been developed under the auspices of the GMOD project (http://www.gmod.org/), which seeks to create software that may be generically useful for Model Organism Databases (MODs). WHAT DO THEY DO? These modules provide an object oriented set of libraries for dealing with files produced by the Gene Ontology project (GO - http://www.geneontology.org/). In particular, the GO::TermFinder object allows a client program to provide a list of genes, from which it will determine p-values for the annotation associated with that list of genes. It does this using the hypergeometric distribution. In addition, a corrected p_value is calculated, to correct for multiple hypothesis testing. Two simple clients of these modules are provided in the examples directory. INSTALLATION To install this module type the following: First decompress the gzipped tarfile, e.g: tar zxvf GO-TermFinder-0.21.tar.gz Then cd into the created directory, e.g.: cd GO-TermFinder-0.21 Then actually install it: perl Makefile.PL make make test make install The make install step will require, on most unix systems, that the command be run with root privileges, as by default it will install the libraries in a location (usually something like ${PERL5LIB}), which requires root privileges to write there. If you want to install the libraries in an alternative place, such as your home directory, do: perl Makefile.PL INSTALLDIRS=site INSTALLSITELIB=/home/your/private/dir as the first step of the installation, where /home/your/private/dir is obviously your target destination. Note for the example scripts to work you will have to add: use lib "/home/your/private/dir" before the other use statements. DEPENDENCIES This module requires these other modules and libraries: Storable CONTACT INFO If you have any suggestions, bug fixes, etc, please post them to the gmod site at http://www.gmod.org/, or send email to sherlock@genome.stanford.edu. Note The ontology files in the t/ directory are solely for the purposes of running the test suite. You should get the latest versions from the Gene Ontology website for your own analyses. COPYRIGHT AND LICENCE (the 'MIT license') Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Copyright (C) 2003 Gavin Sherlock, Stanford University