RISOTTO motif discovery tool

Supplementary material

Nadia Pisanti, Alexandra M. Carvalho, Laurent Marsan and Marie-France Sagot


If you use RISOTTO in your research, please cite:

If you use RISO in your research, please cite:


RISOTTO is an extension of RISO-Dynamic with maximum extensibility improvement (Linux executable [bin] and sources [src]).

Compile and run

To compile RISOTTO:


Set up the input

RISOTTO 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 RISOTTO discovers in the input dataset, it prints the following information:

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

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

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

An example

Go to RISOTTO 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 .