PPH1 
===============

Written by: Olivier Mirabeau
Date:    Feb 2007

relevant publication
-----------
Mirabeau et al. 
"Identification of novel peptide hormones in the human proteome by hidden Markov model screening"
Genome Research, March 2007

Description
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PPH1 is a java program which implements a hidden Markov model of peptide hormone precursor sequences. It takes Clustalw alignments as inputs.
This program can be used to screen animal genomes for peptide hormone precursor sequences.

Arguments
-----------
usage: bat\pph1.bat ali_files_directory main_directory output_directory
The program takes as input three arguments: 
1) the path to the directory where the input alignments are stored (ali_files_directory)
2) the path to the directory where the pph1.jar jar file is locate 
3) the ouput directory where the prediction file "pred.xml" is written. 

example of program execution (using the .bat file on Windows): 
bat\pph1.bat D:\GR2007_Supplemental\pph1\examples_aln D:\GR2007_Supplemental\pph1 D:\GR2007_Supplemental\pph1\predictions

Output
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A predicted features file "pred.xml" (signal peptide, cleavage site,.. cf GR 2007 paper). This prediction file can be browsed using the DTD "hmmpred.dtd". For that make sure that the path indicated in the second line of "pred.xml"  matches that of "hmmpred.dtd" (that is located in the "predictions folder").


Notes
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- The pph1 hidden Markov model is described in the file "HMMGLOBALMODELFURIN4.xml". Its associated DTD is "hmm1.dtd". 
- The folder "examples_aln" are examples of ClustalW-format alignment files that can be used as inputs for pph1.


INSTRUCTIONS FOR RUNNING IT ON A WINDOWS SYSTEM:
-----------
- copy the "pph1" folder into a folder with path="DIRECTORY" (this is the working directory)
- edit the "pph1.bat" in the "bat" folder and 1) replace "C:\Program Files\Java\jre1.8.0_77\bin\java" with the correct path to the java executable and 2) modify the default directory path "E:\GR_2007\GR2007_Supplemental\GR2007_Supplemental\pph1" to match working directory with path "DIRECTORY" 
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contact: 
olivier.mirabeau@gmail.com