gDNA-Prot Files

                               gDNA-Prot RELEASE NOTES
                               =======================

gDNA-Prot program

by Wei Zheng (jlspzw139@sina.com) and Wuyunqiqige

The gDNA-Prot is an effective and fast computational method to predict DNA-binding proteins, which applies
with the support vector machine classifier and two classes feature representation.The detail analysis process
can refer to the paper for gDNA-Prot: predict DNA-binding proteins by employing support vector machine and a 
novel numerical characterization of Protein sequence.

This program will predict the DNA-binding proteins when input a protein sequence (Fasta format), 
it is supplied in source code form along with the required data files and run under the windows.

Firstly we can download the gDNA-Prot.zip in http://sourceforge.net/projects/gdnaprot/. 
Unzip this files, in windows system, open 

my computer->all programs->Accessories->Windows Powershell->Windows Powershell.

In the Windows Powershell, we must run the relevant commands as adminstrator.
Then input the 'Set-ExecutionPolicy Unrestricted' to get the execuate permissions of the Powershell
script. If you want to know much about 'Set-ExecutionPolicy', please run 'Get-Help Set-ExecutionPolicy'.

INPUT FILE: sequence_file in fasta format.

EXAMPLE: 

In current directory, if we will predict a protein sequence, we can run:

.\gDNA-Prot.ps1 -inputfile .\example\newDNAiset.fasta -outputfile iset.out.txt -method pca -type maxmin

to see more help, you can run:

.\gDNA-Prot.ps1 -help help

****************************************************************************************************************************
help:
gDNA-Prot.ps1 -inputfile inputfile_param -outputfile outputfile_param -method method_param -type type_param -help help_param
[option] -inputfile           ----input file path, fasta file;
         -outputfile          ----output file path;
         -method              ----train method, pca or normal, default=pca;
         -type                ----method for normalizing data to [-1,1], maxmin or sigmod, default=maxmin;
         -help                ----get help, h or help; 
example:
.\gDNA-Prot.ps1 -inputfile .\example\newDNAiset.fasta -outputfile iset.out.txt -method pca -type maxmin
.\gDNA-Prot.ps1 -help help
*****************************************************************************************************************************

Please see the LICENSE file for the license terms of the software. It is basically free for academic users, 
but a license fee applies to commercial users. 

THE PUBLICATION OF RESEARCH USING Our method MUST INCLUDE AN APPROPRIATE
CITATION TO THE METHOD:

Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of Protein sequence.