PPIExtend Online Document
PPIExtend is a tool for finding quasi-bicliques in PPI Networks.
PPIExtend is now available for Linux.
PPIExtend is implemented in Java.
To run PPIExtend, Sun's Java Running
Environment (JRE) 6.0 is required. If JRE is not installed, please go to
to download and install the JRE.
1. Download the file PPIE_1.0.0.tar.gz.
2. Extract the downloaded file.
tar xvfz PPIE_1.0.0.tar.gz
3. Make sure that execute permission is set on the setup shell script
chmod +x setup.sh
4. Run the setup shell script
5. Move the shell script PPIExtend to a /bin directory.
mv PPIExtend ~/bin
In the input file, each line contains a pair of interacting proteins. The two protein names are seperated by a space.
For example, see file input_example.txt.
Run PPIExtend with five arguments:
(1) input file name (2) delta (3) tau (4) alpha (5) result file name.
Input file name and result file name are self explanatory.
The three parameters delta, tau and alpha are discussed in the paper.
Delta is a real number. Tau and alpha are two positive integers.
Suppose the input file name is "input_example.txt", the result file name is "result_example.txt", delta = 0.1,
and tau = 5 and alpha = 5. We use
PPIExtend input_example.txt 0.1 5 5 result_example.txt
In the result file, each quasi-biclique is described
using three lines. The first line contains the serial number, the numbers of vertices in two vertex sets.
The second line is the list of the vertices in the the first vertex set and the third line is the list of
vertices of the second vertex set.
For example, see result_example.txt.