CreateBackgroundModel

This page provides access to a database of precompiled background models for
- a list of prokaryotes ;
- Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, Drosophila melanogaster,
- Bos taurus, Gallus gallus, Homo sapiens, Mus musculus, Rattus norvegicus,
- Xenopus leavis, Arthropodes, Echinoderm, Nematodes,
- Plants and Vertebrates.
You can also compile your own background model by running CreateBackgroundModel on your own dataset of carefully selected intergenic sequences.

To optimally run this tool and evaluate its output, please consult our guidelines.
Stand-alone executable: download.

The speed with which results are generated depends on the server load.

Last software revision : . (updated April 21, 2020)

Questions & suggestions: contact us.

Publications:

If you like our software, please use the MotifSuite publication for citing : MotifSuite publication.

If you are using this webpage as a standalone application outside our MotifSuite workflow, you can also use one of the following publications for citing :
- G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, P. Rouze and Y. Moreau. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. 2001. Bioinformatics, 17(12):1113-22.
- K. Marchal, G. Thijs, S. De Keersmaecker, P. Monsieurs, B. De Moor, and J. Vanderleyden. Genome-specific higher-order background models to improve motif detection. 2003. Trends in Microbiology, 11 (2): 61-66.

1) Select a precompiled background model from our database:

Please fill in your email adres, select the organism of interest and choose an appropiate background model order (order 2 will in general be a good choice). Pressing Submit will retrieve the requested background model from our database and the result will be emailed to you.
Attached illustrative example is the background model of order 2 for Escherichia coli(K12).

Your email address, we will mail you the url with the result.
Select the organism and order of the background model : (example Escherichia coli (K12) - order 2)

2) Run CreateBackgroundModel:

To run this application, please fill in the required input in the blank fields. In the output section, a (randomized) file name has been generated. You can overwrite this automatically generated filename with a more meaningful description if desired (do not use spaces, dots, colons,... in this name). The program parameters have been set to a default value. Please analyze if these settings apply to your case (checkout our CreateBackgroundModel Guidelines) and overwrite whenever needed. Pressing Submit will initiate the CreateBackgroundModel software on our server. An url containing the results will be sent by email.

Input:
Your email address, we will mail you the url with the result.
-f <filename>: file with a list of sequences in Fasta format (EvgA example).

Output:
-b <filename>: file with the background model (format, EvgA example).

Parameters:
-o <value>: order of the background model. Default <1>.
-n <name>: identification of the sequences dataset, this is only informational.