cmotif Files

C-Motif:
In this paper, we present a method for mining conditional phoshporylation motifs. C-Motif is implemented in Java and can run on any Java Virtual Machine (JVM) regardless of computer architecture.



How to try the program:

1. Install and run Netbeans into your computer.
Important prerequisite: you must first install the Java Development Kit (JDK).

2. Download the source codes from this website into your computer.
Click on the link http://sourceforge.net/projects/cmotif/ to download C-Motif.zip into the folder you chose as the workspace and decompress the project.


3. Execute C-Motif with Netbeans.
You can use the Wizard to import the C-Motif project into workspace. 
	From the main menu bar, select " File > Open projects". 	The wizard opens.  
	Choose "Select root directory" and click the associated "Browse" to locate the directory where you put the project. 
	Under "Projects" select the C-Motif project to open. 
 

Select CMotif.java and start the Java program.

The input data is put in the folder "data". You can change the file name in the main function to run your own data.



Input and output files.

1. Input files

Non-kinase-specific phosphorylation data: This folder contains two files which are the foreground data consist of non-kinase-specific phosphorylated peptides and the background data consist of unphosphorylated peptides.
 
CDK-specific phosphorylation data: This folder contains two files which are the foreground data consist of CDK-specific phosphorylated peptides and the background data consist of unphosphorylated peptides. 

PKA-specific phosphorylation data: This folder contains two files which are the foreground data consist of PKA-specific phosphorylated peptides and the background data consist of unphosphorylated peptides. 


2. Output files
ResultByC-Motif		output file with the conditional phosphorylation motifs under some parameter setting the users have set.
DetailedFinalResultByC-Motif   output file with the condition phosphorylation motifs and their corresponding global and local significance values.

3. Other input and output files whose formats are similar to the samples are also accepted.