SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically drive

Background: Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma () Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations. Results: We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and 10 boxes. These patterns are then grouped using pairs of short seeds (of which on...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond
• Keywords: BMCBI 2008, Factor Binding Sites, Related Bacterial Genomes, Variable Spacer Lengths