RISO motif discovery tool

Supplementary material

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot


If you use RISO in your research, please cite:

If you use RISOTTO in your research, please cite:


Three implementations of RISO were developed:

Compile and run

To compile RISO:

To run RISO:

Set up the input

RISO discovers motifs composed of many binding sites separated by spacers. Each binding site is called a box.

Generic parameters:

For each box of the motif it is also needed:

An example of the input parameters follows:

Alphabet file        ../params/alphabet
FASTA file           ../params/dnc_subtilis_330-30.seq
Output file          ../params/b-subtilis-output
Quorum               12
Boxes                2

Min length           6
Max length           6
Substitutions        1
Min spacer length    16
Max spacer length    18
Min length           6
Max length           6
Substitutions        1

Interpret the output

For each motif that RISO-Dynamic discovers in the input dataset, it prints the following information:

RISO-Static outputs only the motifs and the number of different sequences where the motifs appears.

An example of the output follows:

%%% 2 128/1062 196736 12 12 2 6 6 1 16 18 6 6 1 alphabet ACGT$

AAAAAA_AAAAAA 000000-000000 188 703
AAAAAA_AAAAAC 000000-000001 139 357
AAAAAA_AAAAAG 000000-000002 166 410
AAAAAA_AAAAAT 000000-000003 193 461


TTTTTT_TTTTTA 333333-333330 201 507
TTTTTT_TTTTTC 333333-333331 171 441
TTTTTT_TTTTTG 333333-333332 148 384
TTTTTT_TTTTTT 333333-333333 188 700

Nb models: 6419
User time: 45.33 sec.

Assess statistical significance

RISO-Dynamic is compatible with SMILE statistical significance application. To assess statistical significance within RISO-Dynamic, you have to download the SMILE algorithm, and put the statistical significance applications (e-smile_shuffling and e-smile_against) in the RISO-Dynamic bin directory. An example of statistical assessement with RISO-Dynamic can be found in An example.

If you assess statistical significance of the motifs extracted by RISO-Dynamic in your research, please also cite:

An example

Go to RISO params directory.

Download the input files to that directory:

Type in your terminal:
riso b-subtilis-input

Two output files should be created:

For any help please contact Alexandra M. Carvalho at .