In the post-genomic area, the prediction of transcription factor regulons by position weight matrix-based programs is a powerful approach to decipher biological pathways and to model regulatory networks in bacteria. In 2007 we developed PREDetector1 (Prokaryotic Regulatory Elements Detector), a tool designed to predict regulons of DNA-binding proteins in bacterial genomes. Beside the automatic prediction, scoring and positioning of potential binding sites and their respective target genes in annotated bacterial genomes, the software also provides statistical data in order to assess the reliability of predictions. Finally, PREDetector is able to generate a position weight matrix based on the input sequences and on GC content (given or computed from the sequences’ GC content). Version #1 of PREDetector has been downloaded about 400 times (http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php) and is routinely used in microbiology research groups. Based on the feedback and the comments of the numerous users PREDetector, we now aim at improving this service by, amongst other, 1) creating a web-based service where users could perform predictions in real time, while limiting this service to a maximum of 10 simultaneous users to prevent a too long response time 2) to change the sequence database to access annotated genomes (from NCBI to PATRIC which is more exhaustive), and, more importantly, 3) to implement the software in order to perform simultaneous predictions in closely related microorganism. The main difficulty in this third part is the use of an external ortholog database to be able to match the different annotations for the same gene.

References: Hiard S, Marée R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel GP, Joris B, Wehenkel L, Rigali S. (2007). PREDetector: A new tool to identify regulatory elements in bacterial genomes. Biochem Biophys Res Commun. 357(4):861-4.

Supervisors: Sébastien Rigali, Louis Wehenkel, and Samuel Hiard