Short Explanation of Each Program and File:

1. OMiMa -- the main program file for motif identification
2. OMiMa.conf -- an example configure file for OMiMa
3. OMiMa_Readme.pdf -- Short User Instruction of OMiMa 
4. E2F*.* -- Example files for the program HistPlot at the following
5. HistPlot -- the program creates histogram plots using the histogram
            data (Location data and score data) output from OMiMa. 
	    Its usage is given below:

         Usage:./HistPlot inFolder InFiles graphFormt xLabel YLabel [numOfBin]

	Example 1: single file mode
		
		To plot location histogram of TfbsOne that :
		1)  Input file is TfbsOne.loc
		2)  Input file is in directory ./file_path  
		3)  Output histogram is EPS figure  
		4)  x-axis label is "Location" and Y-axis is "Frequency"
		
		The plot command will be:		
		./HistPlot ./file_path TfbsOne.loc eps Location Frequency

	Example 2: Multiple files mode

		To plot histogram of several files whose filenames end with same suffix, e.g. *.loc, 
		and output histogram is PNG figure
		The plot command will be:		
		./HistPlot  ./file_path loc png Location Frequency

	Example 3: a real example 

		In the current directory, we have two histogram data files of E2F TFBS found 
		in the Human Genome by OMiMa: 
		 1) E2F.loc -- Relative Location of E2F TFBS Transcription Start Site (TSS) 
		 	The histogram plots: E2F-loc.eps and E2F-loc.png were created by the
			following two commands, respectively.
			 ./HistPlot . E2F.loc eps  "Relative Location to TSS" Frequency 25
			 ./HistPlot . E2F.loc png  "Relative Location to TSS" Frequency 25

		 2) E2F.score -- Log-likelihood scores of E2F TFBS to Transcription Start Site
		 	The hisogram plots: E2F.eps and E2F.png were created by the
			following two commands, respectively.
			./HistPlot . E2F.score eps  "Log-likelihood Score" Frequency 20
			./HistPlot . E2F.score png  "Log-likelihood Score" Frequency 20


Citation for OMiMa:
	Weichun Huang, David M Umbach, Uwe Ohler and Leping Li.
	Optimized mixed Markov models for motif identification.
	BMC Bioinformatics 2006, 7:279 
	
	For Bibtex users:
	@ARTICLE{huang2006,
         author = {Weichun Huang, David M Umbach, Uwe Ohler and Leping Li},
	 title = {Optimized mixed Markov models for motif identification},
	 journal = {BMC Bioinformatics},
	 year = {2006},
	 volume = {7},
	 pages = {279}}

-- Prepared by Weichun
