Table 2.

Information on operon predictions from Rockhopper for ten genomes is shown in the table. The first column indicates the genome. The second column indicates the number of RNA-seq experiments from which Rockhopper used data to make its operon predictions. The third column indicates the number of multi-gene operons (operons containing two or more genes) predicted by Rockhopper. The fourth column indicates the total number of genes in all the multi-gene operons predicted by Rockhopper. The fifth column indicates the total number of protein-coding genes in the genome as annotated by RefSeq [35]. The sixth column indicates the similarity of Rockhopper’s operon predictions to DOOR’s operon predictions [16] as measured by the Rand similarity coefficient [51].

Genome	Number of RNA- Seq Exps	Multi- Gene Operons	Number of Genes Part of some Multi- Gene Operon	Total Genes in Genome	Similarity to DOOR Predictions
Neisseria gonorrhoeae	2	410	1114	1886	91%
Salmonella enterica	4	868	2677	4549	94%
Streptococcus pyogenes	2	412	1307	1693	94%
Escherichia coli	16	838	2557	4386	95%
Caulobacter vibrioides	2	780	1428	3737	92%
Helicobacter pylori	2	301	1111	1448	94%
Pseudomonas aeruginosa	4	1215	3755	5573	92%
Bacillus subtilis	4	880	2765	4328	90%
Shewanella oneidensis	4	724	2169	4266	90%
Vibrio cholerae	2	675	2011	3510	88%