Computational prediction methods are a ''first pass'' genome structural annotation. Whole genome transcriptome studies (such as whole genome tiling arrays [13, 14, 15] and high throughput sequencing [16, 17] ) are complementary experimental approaches for bacterial genome annotation and can identify ''novel'' genes, gene boundaries, regulatory regions, intergenic regions, and operon structures. For example, a transcriptomic analysis of Mycoplasma pneumoniae identified 117 previously unknown transcripts, many of which were non-coding RNAs, and two novel genes [18] . Transcriptome analyses identified novel, non-coding regions in other species, including 27 sRNAs in Caulobacter crescentus [15] , 64 sRNAs in Salmonella Typhimurium [17] , and a large number of putative sRNAs in Vibrio cholerae [16] . sRNAs found in pathogen genomes are known to be involved in various housekeeping activities and virulence [19] .