Supplementary Data
Learn Motif
  From Unaligned Sequences
Download executable

Learn Motifs

This executable currently allows you to learn motifs from unaligned sequences. In the future is will also allow you to learn motifs from aligned sequences and to search motifs in sequences. It is provided as an executable wrapped in Perl scripts, as described below.

NOTE:THIS SOFTWARE IS FREELY AVAILABLE FOR ACADEMIC USE ONLY, and is distributed under the The GNU Lesser General Public License.


  1. The executable is compiled for a 64 bit Linux machine. It is wrapped by Perl scripts.
  2. It requires Java installation (jre is enough) and the $JAVA_HOME environment variable should point to the jre/jdk directory.
  3. The executable uses the weblogo utility under this license, the Xvfb program under this license and Xerces, a third party shared library. You can find its license terms at

Versions History

Last version is available here for download.
  • Version 1 (23-Jun-08): Initial release.
  • Version 2 (21-Dec-08):
    • Improved randomization.
    • An option to provide the randomization seed, so the randomization is reproducible.
    • Reverse complement motifs (gxw and logo files) are generated.
    • Small technical issue regarding drawing of the FMM logos.

Download Instructions

  1. Download the archive file into a folder of your choice. 64-bit version: .
  2. Unzip and extract all its files (tar xvfz 64bit_exe_fmm08_motif_finder.tar.gz).
  3. Type make install


The main script is, type: --help to see its usage.

The main parameters the script expects are:
  • Positive sequences file - a fasta format file containing the sequences bound by a TF.
  • Negative sequences file - a fasta format file containing the unbound sequences.

The download zip file contains example files:
  • input_pos.fa - example positive sequences file
  • input_neg.fa - example negative sequences file
  • Output - directory with all the output files. The motif_hits.html in that directory contains links to all the output files.
These output files were produced by this command:
./ -p input_pos.fa -n input_neg.fa -output_dir Output

For troubleshooting and FAQ please visit our executables FAQ page and the paper FAQ Page.