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PPWMs

PPWMs: is a tool for predicting palmitoylation sites based on protein sequence. The program is implemented in C. The win32 console version is provided. (You could Right-Click [Code] , and Save, then you can download the whole matlab code.)

Reference

Y.-X. Li, Y.-H. Shao, N.-Y. Deng. Improved Prediction of Palmitoylation SitesUsing PWMs and SVM[J]. Protein \& Peptide Letters,2011, 18(2): 186-193(8).

• 1. Input File
  
  The input file is in the FASTA format. Each file can includes one or multiple sequences. Each sequence must have the amino acid "C". More sequences require more computer resource. For typical computer, the number of sequences less than 50 should be fine.
  
  The output will be saved into "Result.txt" in the same directory.
  
  
  • 2. Command Line
    
    PPWMS <Input File> <Cutoff>
    
    where <Input File> is specified above. The Cutoff should be "Low", "Medium" and "High" correspoding to differernt true positive rates respectively.
    
    The input file is in the FASTA format. Each file can includes one or multiple sequences. Each sequence must have the amino acid "C". More sequences require more computer resource. For typical computer, the number of sequences less than 50 should be fine.
    
    The output will be saved into "Result.txt" in the same directory.
    
    
    • 3. For examle:
      
      PPWMs P49802.fasta Low

      
      Download from:

      PPWMs.rar

      
      
      
      

      Contacts

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      Any question or advice please email to shaoyuanhai21@163.com.

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      • Last updated: April 5, 2013