Command Line MotifComparison

Overview

1. Required arguments
2. Optional arguments
3. Background model description

Switch	Argument	Description
-m	matrix file	File with the query motif models. A description of the format of a motif file can be found below.
-d	matrix file	File with motif models to which the query motifs will be compqred. A description of the format of a motif file can be found below.

Switch	Argument	Description
-o	file	The output is a tab-delimited ascii text file. Each line contains the query motif identifier, query motif consensus, database motif identifier, database motif consensus and similarity score.
-t	value	Threshold between 0 and 1. If the Kullback-Leiber distance between two motifs is smaller than this threshold these motifs are considered as similar.
-s	value	Allowed shift to compare two motifs.

A set of pre-compiled motif models should be stored in an ascii text file using a well defined (and not very flexible) format. Such a file can be the result of the MotifSampler.
Below you can find an example of the a motif model file with 2 motifs. The file should always start with the word #INCLUSive at the first position of the file. For each motif the lines staring with "#ID" and "#W" are obligatory, while the lines starting with "#Score" and "#Consensus" are optional. After the identifiers, the data matrix itself is represented. There should be always 4 columns separated by a tab or white spaces. The matrxi should count as many rows as stated by the value in the preceeding line starting with "#W".

--
#INCLUSive Motif Model v1.0
#
#ID = gbox
#Score = 274.657
#W = 8
#Consensus = nmCACGTG
0.1857  0.0559  0.5727  0.1857        
0.3518	0.5912  0.0559  0.0011      
0.0011  0.9973  0.0005  0.0011      
0.9979  0.0005  0.0005  0.0011      
0.0011  0.9973  0.0005  0.0011      
0.0011  0.0559  0.9419  0.0011      
0.0011  0.0005  0.0005  0.9979        
0.0011  0.0374  0.9604  0.0011      


#ID = sigma54
#Score = 91.5958
#W = 16
#Consensus = TGGCACrAnnnnTGCw
0.00575087      0.00400983      0.00393972      0.9863  
0.00575087      0.00400983      0.984465        0.00577424      
0.00575087      0.00400983      0.984465        0.00577424      
0.00575087      0.984535        0.00393972      0.00577424      
0.986276        0.00400983      0.00393972      0.00577424      
0.00575087      0.682835        0.00393972      0.307474        
0.458301        0.00400983      0.45649         0.0811993       
0.684576        0.30571         0.00393972      0.00577424      
0.232026        0.30571         0.0793647       0.382899        
0.382876        0.15486         0.15479         0.307474        
0.307451        0.30571         0.15479         0.232049        
0.156601        0.15486         0.15479         0.533749        
0.00575087      0.00400983      0.00393972      0.9863  
0.00575087      0.00400983      0.90904         0.0811993       
0.0811759       0.75826         0.00393972      0.156624        
0.609151        0.00400983      0.00393972      0.382899        

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