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           Regulatory modules using evolutionary Monte Carlo          
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EMCMODULE is a program to find regulatory modules using evolutionary
Monte Carlo. To use the program, save the linux or unix executable as 
applicable as a file "emcmodule" in your directory, and  type 

./emcmodule

at the linux or unix command prompt.

To find details regarding input options, type

./emcmodule help

EMCMODULE requires as its input a fasta formatted file of upstream sequences,
and a file containing start set of motifs (and their locations on sequences)
in the formatted columns

MotifIndex 	SequenceNumber	PositionOnSequence 	MotifSite

If such a file is not available, you may use, for example, BioProspector 
(http://bioprospector.stanford.edu/) or MEME to get an initial set of
motifs. Two perl scripts are ("extractBPmotifs.pl" and 
"extractMEMEmotiflist.pl") provided here to extract the motif list in 
required format from BioProspector and MEME output, respectively. (for
no reason other than my personal bias!) However, there is nothing
against your using your favorite motif finder to find an initial set
and supply it as input to emcmodule- as long as it conforms to the
correct input format.  

For examples of input motif list and input sequence file formats, check out 
the files "test.sites" and "test.fasta"; a sample output file is given
in "t.out".

The commands to use the perl scripts are:

extractBPmotifs.pl  bioprospector.outputfile motifwidth emcms.startset
extractMEMEmotifs.pl  meme.outputfile  emcms.startset

(IMPORTANT NOTE: MEME output must be in PLAIN TEXT FASTA FORMAT
Please choose the options " -dna  -print_fasta -text " when running MEME)

For further questions, please contact Mayetri Gupta (gupta@bios.unc.edu)