Table 6.

Comparison of three ncRNA detection programs on a whole genome screen using the MUMmer alignment.

	probability cutoff for ncRNA classification
	P > 0.5		P > 0.9		P > 0.99
	Dynalign	RNAz	Dynalign	RNAz	Dynalign	RNAz	QRNA
Known ncRNAs found (percent of total known ncRNAs in parentheses)
E. coli (156 ncRNAs known)	128 (82.05)	125 (80.13)	123 (78.85)	104 (66.67)	107 (68.59)	91 (58.33)	67 (42.95)
S. typhi (110 ncRNAs known)	103 (93.64)	98 (89.09)	102 (92.73)	84 (76.36)	93 (84.55)	70 (63.64)	64 (58.18)
Number of contiguous, non-overlapping hits that are not known ncRNAs (i.e. novel ncRNA candidates)
E. coli	1,183	1,255	872	996	578	678	661
S. typhi	1,178	1,255	857	977	568	662	634
Number of nucleotides classified as ncRNA that are not in known ncRNAs (i.e. nucleotides in novel ncRNA candidates)
E. coli (each strand = 4,639,675 nt)	169,580	174,790	123,563	128,343	81,936	80,054	87,577
S. typhi (each strand = 4,809,037 nt)	163,037	174,126	117,277	126,393	76,289	79,713	88,099
Total number of nucleotides classified as ncRNA (i.e. nucleotides in both known and unknown ncRNAs)
E. coli (each strand = 4,639,675 nt)	224,051	222,817	175,174	166,676	129,086	104,428	113,090
S. typhi (each strand = 4,809,037 nt)	213,549	218,867	166,187	162,077	122,269	102,464	114,434

QRNA, RNAz, and the Dynalign/LIBSVM classifier are compared in their ability to detect known ncRNA in the E. coli and S. typhi genomes, based on a MUMmer whole genome alignment. For RNAz and the Dynalign/LIBSVM classifier, results are listed for three P value classification cutoffs. "Number of nucleotides" = number of nucleotides on the plus strand + number of nucleotides on the minus strand, not accounting for overlap of complementary strands.