We analyzed BLAST results manually, to identify novel protein coding regions and start codon corrections. If no protein coding region was found in the intergenic expressed regions, the presence of a promoter or a rho-independent terminator allowed us to classify the regions as sRNA. Bacterial promoter sequences were predicted by Neural Network Promoter Prediction program (http://www.fruitfly.org/seq_tools/promoter.html) [43] . Rho-independent transcription terminators were identified using the program TransTermHP [44] . For functional annotation, all identified identified sRNA sequences were searched against the Rfam database [23] . sRNA sequence conservation among other genomes was determined by blastn searches against nonredundant nucleotide database at NCBI. We mapped sRNAs, along with additional features, onto genome browsers like IGV [45] and Artemis [46] for further visualization, manual analysis, and interpretation.