IGIPT:  Integrated  Genomic   Island   Prediction   Tool


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Programs that Work on the Genome Level:

Instructions to Download and Run the tool
1. Click on the link Genome Based Measures
2. Download all the files and place them in a directory. Unzip the File to obtain a set of 7 executable files.
3. Run the following command to change the file permissions of all the files. For instance if the name of the executable is "gc", then perform the following operation.
    chmod 777 gc
4. When the permissions have been set, run the executable file in the following manner. Here the input file refers to the complete genome sequence.
    ./gc inputfile_name window_size
5. Output will be displayed in excel files. The excel sheets will contain the complete results (without filteration) divided in 4 columns (except GC) describing the window start, window end, mid-point and the values of the respective measure. The GC file contains other information such as GC Skew and G+C Count.
7. Parameters:
    Window Size can vary from 5KB to 20KB or above
    Standard Deviation can vary from 1, 1.5 to 2

Programs that Work on the Gene Level:

Instructions to Download and Run the tool
1. Click on the link Gene Based Measures
2. Go to the directory where the executable file is downloaded. Unzip the File to obtain a set of executable files and perl scripts.
3. Run the following command to change the file permissions in the command line
    chmod 777 cb
4. In the command line run the executable file in the following manner
    ./cb inputfile_name OUTFILE.txt window_size
5. Output will be displayed in excel files.
7. Parameters:
    Window Size can vary from 5KB to 20KB or above
    Standard Deviation can vary from 1, 1.5 to 2



Contact Information: Dr.Nita Parekh,  Assistant Professor; Ruchi Jain
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