Table 2.
The table shows the median value of the differences between the predicted and actual boundaries of structured RNAs using RNAbound and Dotu et al. approaches. The base pair probabilities for single sequences and multiple sequence alignments were computed using RNAfold and PETfold, respectively. Only Rfam families with more than five entries are listed here.
| Window | Family (n) | RNAbound | Dotu et al. | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Single seq. | Multiple seq. | Single seq. | Multiple seq. | ||||||
| Left | Right | Left | Right | Left | Right | Left | Right | ||
| 100 | Single hairpin structures | ||||||||
| miRNA (244) | 0.0 | −2.0 | 4.0 | 1.0 | −2.0 | −3.0 | 1.0 | 0.0 | |
| cisreg (28) | 6.5 | −1.0 | 5.0 | −2.0 | −5.0 | −5.0 | −8.5 | −15.5 | |
| snoRNA (6) | 2.0 | −2.5 | 1.5 | −6.0 | −19.0 | −16.0 | −18.0 | −17.5 | |
| all (279) | 0.0 | −2.0 | 4.0 | 0.0 | −2.0 | −4.0 | 1.0 | −1.0 | |
| Branched structures | |||||||||
| tRNA (185) | −5.0 | −7.0 | −5.0 | −9.0 | 1.0 | −2.0 | 0.0 | −2.0 | |
| all (190) | −5.0 | −7.0 | −5.0 | −9.0 | 1.0 | −2.0 | 0.0 | −2.0 | |
| 150 | Single hairpin structures | ||||||||
| miRNA (642) | 10.0 | 6.0 | 11.0 | 9.0 | −5.0 | −6.0 | −1.0 | −1.5 | |
| cisreg (36) | 13.0 | 19.5 | 9.0 | 7.0 | −0.5 | −3.5 | −5.0 | −8.5 | |
| snoRNA (24) | 8.0 | 6.0 | 5.5 | −1.5 | −27.5 | −29.5 | 7.0 | 3.0 | |
| all (709) | 10.0 | 7.0 | 9.0 | 8.0 | −6.0 | −7.0 | −1.0 | −2.0 | |
| Branched structures | |||||||||
| tRNA (166) | 18.0 | 16.0 | −6.0 | −9.0 | 2.0 | −1.0 | 0.0 | −2.0 | |
| cisreg (6) | 11.5 | 13.5 | −4.5 | 3.0 | −0.5 | −21.5 | −4.5 | 1.0 | |
| snoRNA (13) | 0.0 | −8.0 | 0.0 | −12.0 | −12.0 | −71.0 | −14.0 | −82.0 | |
| all (190) | 14.5 | 14.0 | −6.0 | −9.5 | 1.0 | −2.0 | 0.0 | −3.0 | |
| 200 | Single hairpin structures | ||||||||
| miRNA (661) | 30.0 | 30.0 | 30.0 | 33.0 | −6.0 | −7.0 | −2.0 | 1.0 | |
| cisreg (37) | 35.0 | 35.0 | 33.0 | 29.0 | 5.0 | −4.0 | −5.0 | −16.0 | |
| snoRNA (20) | 24.5 | 8.5 | 12.0 | 5.0 | −52.0 | −4.5 | 7.0 | 3.0 | |
| all (727) | 30.0 | 29.0 | 29.0 | 32.0 | −6.0 | −7.0 | −1.0 | 0.0 | |
| Branched structures | |||||||||
| tRNA (127) | 38.0 | 39.0 | −6.0 | −9.0 | 2.0 | −2.0 | 0.0 | −3.0 | |
| cisreg (9) | 23.0 | 17.0 | 23.0 | 26.0 | −5.0 | 3.0 | 16.0 | 26.0 | |
| snoRNA (61) | 11.0 | −2.0 | −7.0 | −69.0 | −20.0 | −24.0 | −18.0 | −86.0 | |
| all (206) | 23.0 | 18.5 | −6.0 | −11.5 | −14.5 | −12.5 | −14.0 | −9.0 | |