GPCRsort v1.0

The GPCRsort package is obtained from
	Mehmet Emre SAHIN, e1395516@ceng.metu.edu.tr,
	http://bioserver.ceng.metu.edu.tr/GPCRsort

******   PLEASE DO NOT REDISTRIBUTE THE PACKAGE   ******

This software is provided ``AS IS'' and any express or implied
warranties, including, but not limited to, the implied warranties of
merchantability and fitness for a particular purpose, are disclaimed.
In no event shall the author be liable for any direct, indirect,
incidental, special, exemplary, or consequential damages (including,
but not limited to, procurement of substitute goods or services; loss
of use, data, or profits; or business interruption) however caused and
on any theory of liability, whether in contract, strict liability, or
tort (including negligence or otherwise) arising in any way out of the
use of this software, even if advised of the possibility of such
damage.

DEPENDENCIES:
=============

The scripts can be run under Microsoft Windows.

Weka 3.6: Data Mining Software in Java is needed. WEKA_HOME environment 
variable must be set to execute the scripts.

Ex: WEKA_HOME=C:\Program Files\Weka-3-6

To make predictions, output of the TMHMM Server v.2.0 is needed. The class 
of only one GPCR can be done. Output ofrmat of TMHMM software must be 
chosen as: 'One line per protein'.

Also Microsoft .NET Framework 3.5 is needed to make predictions.

INSTALLATION:
=============

The package is packed with zip.

It unpacks in a directory called GPCRsort

The directory contains these files:

    README.txt                            This file
	GPCRsort.bat                          a batch script to run the program
	bin/experiments.bat                   a batch script used by GPCRsort.bat
	bin/predict.bat                       a batch script used by GPCRsort.bat
	bin/findClass.bat                     a batch script used by predict.bat
	bin/ LengthCalcFromTMHMMResults.exe   binary executable used by predict.bat
	data/                                 datasets

After unpacking the directory you should

1. Set WEKA_HOME environment variable
2. Run the program as

Usage: GPCRsort.bat -t <1|2|3>
       <to execute experiments>
       <where 1: Cross validation experiment (Section 3.2)>
       <      2: Independent dataset experiment (Section 3.3)>
       <      3: Comparison with other methods experiment (Section 3.4)>

   or  GPCRsort.bat -p <TMHMM_result_file> <depth>
       <to predict the class of an unknown GPCR>
       <where TMHMM_result_file: Result file of prediction of transmembrane helices in GPCR by TMHMM>
       <                         Output format of TMHMM must be: 'One line per protein'>
       <      depth: prediction depth in the GPCR class hierarchy>
       <             values: 0 (exact class) | 1 | 2 | 3>
	   
	   
Mehmet Emre SAHIN
e1395516@ceng.metu.edu.tr
