PREDetector: a new tool to identify regulatory elements in bacterial genomes.
In the post-genomic area, the prediction of transcription factor regulons by position weight matrix-based programmes is a powerful approach to decipher biological pathways and to modelize regulatory networks in bacteria. The main difficulty once a regulon prediction is available is to estimate its reliability prior to start expensive experimental validations and therefore trying to find a way how to identify true positive hits from an endless list of potential target genes of a regulatory protein. Here we introduce PREDetector (Prokaryotic Regulatory Elements Detector), a tool developed for predicting regulons of DNA-binding proteins in bacterial genomes that, beside the automatic prediction, scoring and positioning of potential binding sites and their respective target genes in annotated bacterial genomes, it also provides an easy way to estimate the thresholds where to find reliable possible new target genes. PREDetector can be downloaded freely at http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php.
Hiard
Samuel
S
Department of Electrical Engineering and Computer Science, University of Liège, B28 Systems and Modeling, Grande Traverse 10, 4000 Liège, Belgium. S.Hiard@ulg.ac.be
Marée
Raphaël
R
Colson
Séverine
S
Hoskisson
Paul A
PA
Titgemeyer
Fritz
F
van Wezel
Gilles P
GP
Joris
Bernard
B
Wehenkel
Louis
L
Rigali
Sébastien
S
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D012985:Software Design; D014158:Transcription, Genetic / Q000235:genetics*; D014584:User-Computer Interface