PROMOT

A tool for finding functional motifs from aligned protein sequences

Brought to you by: akashnag

Downloads: 0 This Week

Last Update: 2016-04-16

Get an email when there's a new version of 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

Project Activity

See All Activity >

Follow PROMOT

PROMOT Web Site

Other Useful Business Software

8 Monitoring Tools in One APM. Install in 5 Minutes. Icon

8 Monitoring Tools in One APM. Install in 5 Minutes.

Errors, performance, logs, uptime, hosts, anomalies, dashboards, and check-ins. One interface.

AppSignal works out of the box for Ruby, Elixir, Node.js, Python, and more. 30-day free trial, no credit card required.

Start Free

Rate This Project

Login To Rate This Project

User Reviews

Be the first to post a review of PROMOT!

Additional Project Details

Registered

2016-03-26

Report inappropriate content

Go From AI Idea to AI App Fast

One platform to build, fine-tune, and deploy ML models. No MLOps team required.

Access Gemini 3 and 200+ models. Build chatbots, agents, or custom models with built-in monitoring and scaling.

Try Free

Recommended Projects

Bracelet Generator
A friendship bracelet pattern designer.
JarInspector
JarInspector is a swing based tool. JarInspector scans directories for jar Files and displays all content (classes) of these jar Files in a window. You can sort the content either by classnames or jar Filenames andsearch for classes in the result.
Capsule
Dead-simple packaging and deployment for JVM apps
Java UML Generator (JUG)
Tool for automatic generation of UML Class Diagrams out of Java Class Files. Originally designed as a command line tool to convert .class/.jar files into .emf/.eps files, it now offers a visual environment.
trj_cavity
trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC. The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in https://sourceforge.net/p/trjcavity/wiki/Home/#ffad If you need support using this tool (or report bugs), please post it in the discussion forum. Remarks: v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1.