MotifLab is a general workbench for analysing regulatory regions and discovering transcription factor binding sites and cis-regulatory modules in DNA sequences. For more information, including screenshots and examples, please visit the project web site at www.motiflab.org
MotifLab version 2.0 is currently under development and is still considered to be in "pre-release" stage.
MotifLab is written in Java. To build the project from source you will need:
- Java JDK 8 - programming language
- Maven - build and dependency manager
To compile the Java files and package the project, go to the directory containing the "pom.xml" file and run the Maven command:
mvn package
Maven will package MotifLab into a JAR-file and place it in the "target" subdirectory. The "motiflab-2.0-standalone.jar" file is a "fat" JAR that also includes all external dependencies that are required to run MotifLab. The second JAR-file named "motiflab-2.0.jar" only contains the core MotifLab code, but the external dependencies can be found in the directory "target/lib".
To start MotifLab, go into the "target" directory and run:
java -jar MotifLab-2.0.jar
This will start up MotifLab with the normal graphical user interface. On some operating systems you may also be able to start MotifLab simply by double-clicking the JAR-file.
You can choose a simpler graphical interface with the command:
java -jar MotifLab-2.0.jar -minimalGUI
MotifLab can also be run as a command-line tool without a graphical user interface. In this case you must supply a protocol file that describes the operations to be performed and a file defining which sequences to run the analysis on (unless these are specified in the protocol itself).
java -jar MotifLab-2.0.jar -cli -p <protocol_file> [-s <sequence_file>]
- Kjetil Klepper (kjetil.klepper@ntnu.no)
MotifLab was originally developed as a PhD-project by Kjetil Klepper under the supervision of Professor Finn Drabløs at the Norwegian University of Science and Technology (NTNU). A scientific paper was published in BMC Bioinformatics.
The project was created with NetBeans IDE using the Swing Application Framework for some of the GUI design. The SAF framework is no longer supported by NetBeans (as of version 7), but it is still possible to compile the code.