| 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 |