jPREdictor was developed foremost for the prediction of cis-regulatory elements. Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence. Please refer to the manual on how to use the program for the prediction of regulatory elements.

Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms. The tool jPREdictor is for the fast and versatile prediction of cis-regulatory elements on a genome-wide scale. The prediction is based on clusters of individual motifs and arbitrary combinations of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices. Cluster scores are weighted occurences of multi-motifs, where the weights are derived from positive and negative training sets.

1. Command line tool: Start it with
java -jar jPREdictor.jar -h
java -jar jPREdictor.jar -hs
java -jar jPREdictor.jar -ho
to get help on the all parameters available, special tasks or how to create an option file, respectively.

2. Graphical user interface (GUI): Start the program in the command line with
java -jar jPREdictor.jar

3. Applet: either use your browser and open the file 'jPREdictorApplet.html' or start the applet viewer:
appletviewer jPREdictorApplet.html
If you trust the applet it looks the same like the GUI, if not, no Browse buttons are available and even copy/paste operations are limited.

Requirements:
* Java Runtime 1.5 or above

The license of this software is Freeware, you can free download and free use this calculator software.