MFMD is a computational algorithm for de novo motif discovery. It uses heuristic approaches as a local optimizer and an algorithm based on the MEMES theory as a global optimizer.
Follow the instructions below to be able to run mfmd.
Before running MFMD, you must install the following external programs: Java JRE 8 or higher, WEBLOGO and R. For details about how to install these packages, go to:
- JAVA: www.java.com;
- WEBLOGO: http://weblogo.threeplusone.com/;
- R: https://www.r-project.org/.
After installing the R package, you must initialize the server with the following command:
R CMD Rserve
No MFMD installation procedure is required. After downloading the mfmd.jar, just run the following command line:
java -jar mfmd.jar <dataset_name> <motif width> <significance level>
To test MFMD, download mfmd.jar and the dataset_crp.fasta into a directory of your choice. After that, open a terminal and run:
Java -jar mfmd.jar dataset_crp.fasta 22 0.005
MFMD will create a directory called MDMF_OUT. Inside it, there will be three files:
- logo.pdf: sequence logo of motifs found;
- mfmd_out.txt: summary of the information that the algorithm discovered;
- msa.txt: fasta file with motifs found.
- Jader M. Caldonazzo Garbelini
- André Yoshiaki Kashiwabara
- Danilo Sipoli Sanches
The authors would like to thank CNPq (under grant number 458598/2014-3) for the financial support given to this research.