Table 7.
Comparison of three ncRNA detection programs on a whole genome screen using WuBLASTn genomic windows.
| 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) | 147 (94.23) | 148 (94.87) | 141 (90.38) | 140 (89.74) | 128 (82.05) | 124 (79.49) | 121 (77.56) |
| S. typhi (110 ncRNAs known) | 109 (99.09) | 108 (98.18) | 107 (97.27) | 106 (96.36) | 103 (93.64) | 95 (86.36) | 100 (90.91) |
| Number of contiguous, non-overlapping hits that are not known ncRNAs (i.e. novel ncRNA candidates) | |||||||
| E. coli | 2,569 | 1,898 | 1,828 | 1,568 | 1,211 | 1,257 | 1,403 |
| S. typhi | 3,936 | 2,503 | 2,440 | 1,986 | 1,520 | 1,520 | 1,611 |
| 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) | 324,033 | 275,704 | 235,227 | 221,802 | 167,157 | 174,682 | 206,840 |
| S. typhi (each strand = 4,809,037 nt) | 514,650 | 387,099 | 352,039 | 296,608 | 235,018 | 220,485 | 248,724 |
| Total number of nucleotides classified as ncRNA (i.e. nucleotides in both known and unknown ncRNAs) | |||||||
| E. coli (each strand = 4,639,675 nt) | 385,611 | 332,000 | 292,940 | 270,267 | 220,352 | 209,807 | 242,534 |
| S. typhi (each strand = 4,809,037 nt) | 570,994 | 436,137 | 405,022 | 338,254 | 283,999 | 250,610 | 283,508 |
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 genomic scanning windows prepared using WuBLASTn. 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.