RT Journal Article SR Electronic T1 PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool JF bioRxiv FD Cold Spring Harbor Laboratory SP 084780 DO 10.1101/084780 A1 Pierre Tocquin A1 Aymeric Naômé A1 Samuel Jourdan A1 Sinaeda Anderssen A1 Samuel Hiard A1 Gilles P. van Wezel A1 Marc Hanikenne A1 Denis Baurain A1 Sébastien Rigali YR 2016 UL http://biorxiv.org/content/early/2016/11/01/084780.abstract AB In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.