Design-Island: A Win32 program for detecting Genomic Islands in prokaryotes.
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Contacts: Raghunath Chatterjee (raghuchatterjee@gmail.com), Keya Chaudhuri (kchaudhuri@iicb.res.in), Probal Chaudhuri (probal@isical.ac.in).
           
Refernce: Chatterjee, R; Chaudhuri, K & Chaudhuri, P. "On detection and assessment of statistical significance of Genomic Islands." BMC Genomics 2008, 9:150.


Usage: The program starts with the following options-

Design-Island: for detecting Genomic Islands

Which distance measure do you want to use:
1. Absolute distance (Without Markov model):
2. Euclidean distance (Without Markov model):
3. Kullback-Leibler divergance (Without Markov model):
4. Absolute distance (With Markov model):
5. Euclidean distance (With Markov model):
6. Kullback-Leibler divergence (With Markov model):

 Enter Your choice (1/2/3/4/5/6):-

# On choosing an option from 1-6 the following window will show up #

 1. Island-I (first phase)

 2. Island-II (refinement phase)

 Enter Your choice (1/2) :-

# Enter 1 for running Island-I, which is the first phase of the program. 
  Enter 2 for running Island-II, which is the second phase or the refinement phase of the program. 

For option 1 the program will ask for the following values #

Please enter the parameters for Island-I		
Enter the size of k-tuples:
#e.g., 4#				              
Enter the Initial Probing Window size:		
#e.g., 5000#				              	
Enter no. of Random Samples to be drawn:
#e.g., 200#
Enter the size of the overlapping probing window:
#e.g.,500#
Enter Increment of the probing window: # Probing window will be incremented upto 20000 bp #
#e.g.,500#
Enter the Genome sequence filename (in plain text format):	
#e.g.,aaeol.txt#

# Output will come in the form of a text file as for example: 

20000	250000	5.22731e-006
20000	350000	0.000615492
20000	570000	0.0710692
20000	730000	0.0672469
20000	1.11e+006	0.000311742
20000	1.31e+006	0.00528772
20000	1.33e+006	0.086498
20000	1.37e+006	0.0321793 #

# Where the the first column is the size of the initial probing window, the second column shows the position of the window and the third column shows the P-values. 

Then the program will prompt for the following parameters #

First phase of Design-Island completed
Please enter the parameters for detecting Islands above a cut off P-value:
Cut off P-value:
#e.g., 0.05#
No. of overlapping windows:
#e.g., 5#

# On completion it will generate a file named Ab-first-Islands.txt (if you choose Absolute distance) and will show the following message #
 
No Islands found with these parameters. #If no islands found#
Do you want to use other values?[Y/N]:

# If the answer is 'yes', press 'y' or press 'n' for 'no'. For 'yes', it will again ask for the cut off P-value and the number of overlapping windows,
 but if the answer is 'no', it will show the following message #

First phase islands file Ab-first-Islands.txt is prepared
Do you want to run refinement phase now?[Y/N]:

# Again if the answer is 'yes', press 'y' or 'n' for 'no'. If the answer is 'no' the program will be terminated #One can run Island-II later. But if the answer is 'yes', it will show the following message #


Please enter the parameters for Island-II
Enter the fixed Probing Window size:
#e.g., 2000#
Enter no. of Random Samples to be drawn:
#e.g., 200#
Enter the size of the overlapping probing window:
#e.g., 1000#

# Once the execution of the refinement phase is over, the following message will be shown #

Refinement phase of Design-Island completed
Please enter the parameters for detecting Islands above a cut off P-value:
Cut off P-value:
#e.g., 0.001#

# Finally the output will come in the form of a text file named Ab-refinement-Islands.txt with content e.g.,

182000	184000
250000	256000
344000	352000
356000	358000
514000	516000
566000	574000
576000	578000
646000	648000
652000	654000
674000	676000
1300000	1302000
1304000	1312000 #

# The first column represents the starting cordinates of the Island, and the second column represents the ending cordinates of the Islands #


# If the refinement phase is executed seperately, option 2 of the main menu has to be entered, which will ask for the following paramenters #

Please enter the parameters for Island-II
Enter the size of k-tuples:
#e.g., 4#
Enter the fixed Probing Window size:
#e.g., 2000#
Enter no. of Random Samples to be drawn:
#e.g., 200#
Enter the size of the overlapping probing window:
#e.g., 1000#
Enter the Genome sequence filename (in plain text format):
#e.g., aaeol.txt#
Enter the first phase Islands filename:
#e.g., Ab-first-Islands.txt#

# Subsequent steps and results are going to be similar to those mentioned earlier. #