Command Line CreateBackgroundModel
- Required arguments
- Optional arguments
- 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 |
value |
Set the order of the background model. Default = 1. |
-n |
value |
Set the name of the organism. Default = unknown. |
Background Model Description |
---|
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
--
This page is maintained by Gert Thijs. Last update 2003/10/10.
Email: gert.thijs@esat.kuleuven.ac.be
Copyright © 2002,2003 KULeuven.