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Author: T. Fiedler

Welcome to the jPREdictor project. The program 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. With version 1.22, two new applications were incorporated into the jPREdictor: motif discovery via motif evolution and the motif clustering. Both tasks can only be started via command-line. Please refer to the manual again to get a brief description on how they function and how they are invoked.

Since 24. Apr 2008 version 1.23 of the jPREdictor is available. Some changes were made to the program, and the motif discovery via evolution and the motif clustering is finally official. Please refer to the history section for further explanations on changes and improvements.

Users of jPREdictor are requested to cite :
Fiedler, Thomas and Rehmsmeier, Marc jPREdictor: a versatile tool for the prediction of cis-regulatory elements, Nucleic Acids Research, 2006
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