Command Line BackgroundScore

Overview

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

Switch	Argument	Description
-f	file	Input sequences in fasta format.
-b	file	Output file in specific format. A description of the background model file can be found below.

Switch	Argument	Description
-o	file	The output is a tab-delimited ascii text file. Each line contains the sequence identifier, sequence length, strand and the probability of the sequence being generated by the background model.
-s	0|1	Choose single (0) or double stranded search (1). Default = 1.

A pre-compiled background model is stored in an ascii text file using a well defined (and not very flexible) format. To create such a background model file from a set of input sequences you can use the tool found on our download page
Below you can find an example of the first-order Arabidopsis thaliana background model file. The file should always start with the word #INCLUSive at the first position of the file. Next, there are several lines describing the organism, data set and order of the background model. Finally the data itself are represented.

--
#INCLUSive Background Model v1.0
#
#Order = 1
#Organism = athaliana
#Sequences = /users/sista/thijs/scratch/DNA/intergenic.tfa
#Path = 
#

#snf
0.3449  0.1581  0.1556  0.3414  

#oligo frequency 
0.3449
0.1581
0.1556
0.3414

#transition matrix
0.3911  0.1516  0.1482  0.3091  
0.3760  0.1703  0.1268  0.3269  
0.3630  0.1389  0.1671  0.3311  
0.2756  0.1678  0.1711  0.3855  
--