Table 5.
Detection of long ncRNAs using scanning windows.
| percent identity of entire alignment | total number of scanning windows | number of scanning windows with P > 0.5 | number of scanning windows with P > 0.9 | number of scanning windows with P > 0.99 | |
| 16S rRNA | |||||
| Borrelia burgdorferi and Bacillus subtilis | 74.5% | 30 | 17 | 12 | 6 |
| Homo sapiens (mitochondrial) and Thermotoga maritima | 39.3% | 30 | 1 | 1 | 0 |
| Archaeoglobus fulgidus and Borrelia burgdorferi | 61.8% | 30 | 22 | 17 | 14 |
| 23S rRNA | |||||
| Escherichia coli and Thermoplasma acidophilum | 59.4% | 57 | 49 | 41 | 37 |
| Bacillus subtilis and Bos taurus | 37.1% | 57 | 35 | 26 | 21 |
| Bacillus subtilis and Thermoproteus tenax | 60.1% | 61 | 3 | 2 | 1 |
The Dynalign/LIBSVM classifier is used to compute P values for sets of 150-nucleotide scanning windows iterating (in steps of 75 nucleotides) through global alignments of three 16S and three 23S rRNA pairs randomly selected from a database [48]. The quantity of windows above three P value cutoffs is listed, indicating that long ncRNAs can be detected with short scanning windows.