UbPred - version 1.0 (November 5, 2009)


Installation
------------

UbPred algorithm was implemented and trained in Matlab 2008a. It was 
subsequently compiled, using the Matlab compiler, into a program that 
can be run outside of the Matlab environment.  

In order to run UbPred an appropriate version of the MCRInstaller (we 
provide Windows and Linux versions) has to be downloaded from 
http://www.ubpred.org. Detailed installation instructions generated by
the Matlab Compiler are provided below, in the MATLAB Compiler section. 


Usage
-----

UbPredDTFile input.fasta output.txt

input.fasta is a set of sequences of interest, in FastA format; 
output.txt is a file that will be created by the program. output.txt 
will contain predictions on all sequences in the input FastA file. 

One input/output combination is included (files sample.fasta and 
sample.txt) for testing purposes. 

The predictor outputs all zeros for sequences shorter than 25 residues
and those that contain any character other than the standard 20 AA. 
All characters other than the standard 20 amino acids 
(ACDEFGHIKLMNPQRSTVWY) should be removed prior to running UbPred.


Additional Information
----------------------
Due to the limitations of Matlab's compiler, several features which were
present in the predictor described in the manuscript (Radivojac et al.,
2009) were removed from the on-line and stand-alone versions. The model
was re-trained using this reduced set of features, which resulted in a  
a slightly lower accuracy of the final predictor included in this 
package. 

Also note that the stand-alone executable version does not allow usage 
of scoring matrices. 


Reference
----------

Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG,
and Iakoucheva LM. "Identification, analysis, and prediction of protein
ubiquitination sites." Proteins: Structure, Function, and Bioinformatics.
78(2):365-380. (2010)


MATLAB Compiler Instructions for Windows
---------------------------------------

1. Prerequisites

* Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you    
  have installed version 7.10.   

* If the MCR is not installed, run MCRInstaller, located in:

  C:\Program
Files\MATLAB\R2009a\toolbox\compiler\deploy\win64\MCRInstaller.exe

For more information on the MCR Installer, see the MATLAB Compiler 
documentation.    

2. Files to Deploy

-UbPredDTB.exe
-UbPredDTFile.zip

3. Definitions

MCR - MATLAB Compiler uses the MATLAB Compiler Runtime (MCR), 
which is a standalone set of shared libraries that enable the execution 
of M-files. The MCR provides complete support for all features of 
MATLAB without the MATLAB GUI. When you package and distribute an 
application to users, you include supporting files generated by the 
builder as well as the MATLAB Compiler Runtime (MCR). If necessary, 
run MCRInstaller to install the correct version of the MCR. For more 
information about the MCR, see the MATLAB Compiler documentation.

4. Appendix 

A. On the target machine, add the MCR directory to the system path    
   specified by the target system's environment variable. 


    i. Locate the name of the environment variable to set, using the  
       table below:

    Operating System        Environment Variable
    ================        ====================
    Windows                 PATH


     ii. Set the path by doing one of the following:

        NOTE: <mcr_root> is the directory where MCR is installed
              on the target machine.         

        On Windows systems:

        * Add the MCR directory to the environment variable by opening 
        a command prompt and issuing the DOS command:

            set PATH=<mcr_root>\v710\runtime\win64;%PATH% 

        Alternately, for Windows, add the following pathname:
            <mcr_root>\v710\runtime\win64
        to the PATH environment variable, by doing the following:
            1. Select the My Computer icon on your desktop.
            2. Right-click the icon and select Properties from the menu.
            3. Select the Advanced tab.
            4. Click Environment Variables.  

        NOTE: On Windows, the environment variable syntax utilizes 
              backslashes (\), delimited by semi-colons (;).