mrb20045/PrESOgenesis

PrESOgenesis is a Support Vector Machine-based classifier to predict the spermatogenesis/embryogenesis/oogenesis related proteins based on 1920 meaningful protein sequence features.

PrESOgenesis

1. Introduction

     PrESOgenesis is a  Support Vector Machine-based classifier  to predict the  
     
     spermatogenesis/embryogenesis/oogenesis  related  proteins  based on  1920  
     
     meaningful protein sequence features. It takes protein/DNA FASTA sequences 
     
     as  input,  and  generate  output  about  the potential of a protein to be 
     
     involved  in spermatogenesis/embryogenesis/oogenesis. PrESOgenesis depends 
     
     on  two programs (libsvm and protr  package in R) and can be run on Linux. 
     
     Also,  it  use  TransDecoder  software  to convert the DNA sequences (mRNA 
     
     transcripts that converted to DNA) to protein.   
   

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 and TransDecoder
         
         software and protr package.
         
     
     		$ gzip -dc PrESOgenesis.tar.gz | tar x 
     
     		$ cd PrESOgenesis
     
    		$ chmod 777  /full/path/to/install.sh
    		
    		$ /full/path/to/install.sh
   

4. Run PrOSEgenesis

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

5. Output

    The results will be stored in PrESOgenesis_resultss.txt. The score represents a 
   
    protein's probability of belonging to the  spermatogenesis/embryogenesis/oogenesis. 
   
    PrESOgenesis applied  a probability  score  >0.5 to designate putative related protein.