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.

Features

Motif discovery
Protein sequence analysis
Protein families
Bioinformatics

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