Table 2. Information for 15 test sequences from five types of short RNA: Qrr, tRNA, 5S ribosomal RNA, THF riboswitch and TPP riboswitch.
| Abbr | Seq | Organism (Seq subtype) | Ref | Len | Acc |
|---|---|---|---|---|---|
| V1 | Qrr | V. cholerae (#1) | (6) | 96 | |
| V2 | Qrr | V. cholerae (#3) | (6) | 107 | |
| V3 | Qrr | Vibrio harveyi (#1) | (7) | 95 | |
| T1 | tRNA | Homo sapiens (Cys) | AC004932 | 72 | 0.00 |
| T2 | tRNA | Sulfolobu tokodaii (Lys) | BA000023 | 74 | 0.45 |
| T3 | tRNA | Oryza nivara (Ala) | AP006728 | 73 | 1.00 |
| S1 | 5S | Escherichia coli | V00336 | 120 | 0.26 |
| S2 | 5S | Acheilognathus tabira | AB015591 | 120 | 0.59 |
| S3 | 5S | Desulfurococcu mobilis | X07545 | 133 | 0.88 |
| H1 | THF | Mitsuokella multacida | ABWK02000009 | 99 | 0.11 |
| H2 | THF | Clostridium botulinum | CP000939 | 101 | 0.43 |
| H3 | THF | Streptococcus uberis | AM946015 | 91 | 0.62 |
| P1 | TPP | Thermoplasma acidophilum | AL445064 | 107 | 0.00 |
| P2 | TPP | Pasteurella multocida | AE004439 | 93 | 0.30 |
| P3 | TPP | Bacillus clausii | AP006627 | 100 | 0.62 |
Accession numbers are given for reference when available, and citations otherwise. The tRNA and 5S rRNA sequences and pseudoknot-free secondary structures were obtained from the comparative RNA website (40). The THF and TPP riboswitch sequences and their consensus secondary structures were obtained from the Rfam database (41,42). MFE secondary structures were predicted by GTfold (43) using default settings. The accuracy was calculated as the F-measure, that is the harmonic mean of the MFE sensitivity and positive predictive value against true positive base pairs in the downloaded structures. Sequences were arbitrarily chosen to span the range of MFE accuracies.