Table 1. Summary of secondary structure predictions.
Prediction number | Software | Method | Comparative | SHAPE data | Max. contact distance = 600 nt |
---|---|---|---|---|---|
1 | RNAstructure | Thermod. | NO | YES | YES |
2 | RNAstructure | Thermod. | NO | NO | YES |
3 | PPfold 3.1 | SCFG | YES | YES | NO |
4 | PPfold 3.1 | SCFG | YES | NO | NO |
5 | GTfold (Aug 2011) | Thermod. | NO | NO | NO |
6 | GTfold (Aug 2011) | Thermod. | NO | YES | NO |
7 | GTfold (Aug 2011) | Thermod. | NO | NO | YES |
8 | GTfold (Aug 2011) | Thermod. | NO | YES | YES |
9 | UNAfold | Thermod. | NO | NO | NO |
10 | UNAfold | Thermod. | NO | NO | YES |
11 | PETfold | Combin. | YES | NO | NO |
12 | RNAalifold | Thermod. | YES | NO | NO |
13 | PPfold 3.1 | SCFG | YES | YES (re-normalized) | NO |
Prediction 1 is identical to the structure published in (7). In SHAPE-driven predictions, unless otherwise indicated, the SHAPE data published in (7) were used without re-normalization. The details for re-normalization used for prediction 13 are described in Supplementary Methods. In phylogenetic predictions, the manually curated HIV-1 alignment, described in Materials and Methods, was used. The full pairing schemes are provided in Supplementary Table S1.