PROMOT

PROMOT (version 4.0) is a bioinformatics tool for discovering motifs (in the PROSITE format) from a set of aligned sequences. To run the tool, you need to have Java 8 installed on your system. Download and execute the JAR without any parameters to know about how to use the tool.

A sample alignment of 91 protein sequences is also provided in the file "aligned.fasta". A sample run of the tool can be seen by using the following command:

java -jar promot4.jar 70 2 n aligned.fasta > output.txt

The above command sets fitness threshold to 70%, number of choices per motif element to 2, and ignores the functional grouping of the amino-acids, asking to input the data from aligned.fasta and redirecting the tool output to output.txt. You can open output.txt to view the results of the execution.