Identification of RITs

The WebGeSTer DB [60], database was used in this study to predict Rho-independent terminators (RITS) in P. atrosepticum SCRI1043 using default parameters. Briefly, no more than three mismatches were permitted within the stem structure and only RIT candidates with the highest ∆G score (∆G < = − 12.0 kcal/mol) were considered. Coordinates for putative RITs were obtained from the WebGeSTer DB, and java scripts were used to extract the sequences 200 nt upstream of the terminators (including the stem loop and tail sequences of the terminator). These sequences were considered as putative sRNA candidates and used in downstream sRNA prediction analysis. Additionally, known sRNAs within the P. atrosepticum SCRI1043 genome sequence were searched in the SIPHT web interface (published annotations) [28].