Command Line MotifRanking

Overview

Required arguments
Optional arguments
Background model description

Required Arguments

Switch Argument Description

-i matrix file File with the motif models. A description of the format of a motif file can be found below.

-o matrix file File with best motif models. A description of the format of a motif file can be found below.

Switch	Argument	Description
-i	matrix file	File with the motif models. A description of the format of a motif file can be found below.
-o	matrix file	File with best motif models. A description of the format of a motif file can be found below.

Optional Arguments

Switch Argument Description

-r value Number of top scoring motifs to be reported.

-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.

-m 0,1 or 2 Select the type of score.
0 = Score defined in matrix file (default)
1 = Consensus score [2+plog(p)]
2 = Information Content [plog(p/p0)] (requires -b)

-b file Background model description. Needed to set signle nucleotide frequency when computing the information content.

-s value Allowed shift to compare two motifs.

Switch	Argument	Description
-r	value	Number of top scoring motifs to be reported.
-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.
-m	0,1 or 2	Select the type of score. 0 = Score defined in matrix file (default) 1 = Consensus score [2+plog(p)] 2 = Information Content [plog(p/p0)] (requires -b)
-b	file	Background model description. Needed to set signle nucleotide frequency when computing the information content.
-s	value	Allowed shift to compare two motifs.

Motif Model Description

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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