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Welcome to the OOgenesis_Pred wiki!

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 |									|
 |                    Oogenesis Protein Predictor by:                   |
 |									|			
 |			Mohammad Reza Bakhtiarizadeh                    |  
 |			        Maryam Rahimi                           | 
 |     		      Abdollah MohaMmadi Sangcheshmeh                   |
 |									|
 | 			   University of Tehran$          		|     
 |									|
 |			Contact: mrbakhtiari@ut.ac.ir    		|
 |									|
 |	  Usage:   /path/to/OOgenesis_Pred  /path/to/sequences.fasta	|
 |______________________________________________________________________|

1. Introduction

     OOgenesis_pred is  a  Support Vector Machine-based classifier  to 
     predict the  oogenesis related proteins based on 1920  meaningful
     protein sequence features.  It  takes  protein FASTA sequences as 
     input, and generate output about the potential of a protein to be  
     involved  in oogenesis. OOgenesis_pred depends  on  two  programs 
     (libsvm and protr package in R) and can be run on Linux.
   

2. Pre-requisite

         It just need R software to be installed in your system.
   

3. Install dependencies

         Drag install.sh file to terminal for automatic installing all 
         of  the  dependencies. This will build and install the libsvm 
         software and protr package.
     
     		$ gzip -dc OOgenesis_Pred.tar.gz | tar x 
     
     		$ cd OOgenesis_Pred
     
    		$ chmod 777  /full/path/to/install.sh
    		
    		$ /full/path/to/install.sh
   

4. Run OOgenesis_Pred

     		$ /full/path/to/OOgenesis_Pred    /full/path/to/Candidates.fa
   

5. Output

   The output files will be stored in OOgenesis_Pred_resultss.txt. An example of OOgenesis_Pred output is presented here. The score represents a protein's probability of belonging to the oogenesis. OOgenesis_Pred applied a probability score >0.5 to designate putative oogenesis related protein.

                                                                                ############################   
                                                                                #  OOgenesis_Pred Results  #  
                                                                                #                          #
                                                                                #    21/04/2016 17:30:03   #
                                                                                ############################ 
   
   
    Total number of processed sequences: 3 
    
    Total number of predicted sequences as Ogenesis candidate: 3 
       
    
    __________________________________________________________________________________
    
      Protein_ID	                  Prediction	                  Score	   
    __________________________________________________________________________________
    sp|Q920Q6|MSI2H_MOUSE 	Protein is Ogenesis candidate   	0.595419	 
    __________________________________________________________________________________
    sp|Q9GSX9|RIC8_CAEEL 	Protein is Ogenesis candidate   	0.904385	 
    __________________________________________________________________________________
    sp|P42345|MTOR_HUMAN 	Protein is Ogenesis candidate   	0.682906	 
    __________________________________________________________________________________