Figure 2

Definition of start and stop positions of potential sRNA genes. (a) Workflow for characterization of sRNA genes with the help of bioinformatic promoter analysis at transcriptional start sites (TSS) in library 1 (primary transcripts enriched). All TSS without promoters were removed and the 3′-ends of potential sRNA genes were determined with sequence data from library 2. (b) Library 1 (primary transcripts enriched) was used for definition of transcriptional start sites at 5′-ends of read stacks. The 5′-end of a read stack is defined as a number of read starts that exceed the number of read starts at the previous position by a factor of 20. (c) Weblogo [37] presentations of the consensus sequences of -35 and -10 core regions. In detail, 1267 SigA and 44 SigH promoter sites were detected by the Improbizer tool. The percentage of occurrence of a nucleotide at a particular position is represented by the size of the nucleotide symbol (A, C, G, T).