Table 2 Open in new tab A comparison of... | Oxford Academic

Table 2

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A comparison of prediction accuracies (⁠|$F$|-values) by sequence length for each method

Length	Short (12–150 nt)			Medium (151–500 nt)			Long (501–4381 nt)
	PKF	PK	CB	PKF	PK	CB	PKF	PK	CB
IPknot
(LinearPartition-C)	0.681	0.552	0.258	0.492	0.482	0.128	0.433	0.428	0.061
(LinearPartition-V)	0.669	0.499	0.143	0.478	0.461	0.091	0.380	0.370	0.038
(CONTRAfold)	0.678	0.550	0.259	0.495	0.505	0.154	0.426	0.413	0.066
(ViennaRNA)	0.669	0.500	0.144	0.480	0.461	0.091	0.212	0.317	0.041
ThreshKnot
(LinearPartition-C)	0.681	0.501	0.027	0.493	0.475	0.019	0.439	0.431	0.008
(LinearPartition-V)	0.669	0.484	0.033	0.481	0.456	0.026	0.383	0.372	0.014
Knotty	0.641	0.550	0.315	—	—	—	—	—	—
SPOT-RNA	0.658	0.621	0.322	0.462	0.479	0.127	—	—	—
CONTRAfold	0.682	0.519	0.000	0.500	0.497	0.000	0.425	0.415	0.000
RNAfold	0.668	0.472	0.000	0.474	0.442	0.000	0.361	0.347	0.000

Length	Short (12–150 nt)			Medium (151–500 nt)			Long (501–4381 nt)
	PKF	PK	CB	PKF	PK	CB	PKF	PK	CB
IPknot
(LinearPartition-C)	0.681	0.552	0.258	0.492	0.482	0.128	0.433	0.428	0.061
(LinearPartition-V)	0.669	0.499	0.143	0.478	0.461	0.091	0.380	0.370	0.038
(CONTRAfold)	0.678	0.550	0.259	0.495	0.505	0.154	0.426	0.413	0.066
(ViennaRNA)	0.669	0.500	0.144	0.480	0.461	0.091	0.212	0.317	0.041
ThreshKnot
(LinearPartition-C)	0.681	0.501	0.027	0.493	0.475	0.019	0.439	0.431	0.008
(LinearPartition-V)	0.669	0.484	0.033	0.481	0.456	0.026	0.383	0.372	0.014
Knotty	0.641	0.550	0.315	—	—	—	—	—	—
SPOT-RNA	0.658	0.621	0.322	0.462	0.479	0.127	—	—	—
CONTRAfold	0.682	0.519	0.000	0.500	0.497	0.000	0.425	0.415	0.000
RNAfold	0.668	0.472	0.000	0.474	0.442	0.000	0.361	0.347	0.000

PKF, |$F$|-value for pseudoknot-free sequences; PK, |$F$|-value for pseudoknotted sequences; CB, |$F$|-value of crossing base pairs.

Table 2

Open in new tab

A comparison of prediction accuracies (⁠|$F$|-values) by sequence length for each method

Length	Short (12–150 nt)			Medium (151–500 nt)			Long (501–4381 nt)
	PKF	PK	CB	PKF	PK	CB	PKF	PK	CB
IPknot
(LinearPartition-C)	0.681	0.552	0.258	0.492	0.482	0.128	0.433	0.428	0.061
(LinearPartition-V)	0.669	0.499	0.143	0.478	0.461	0.091	0.380	0.370	0.038
(CONTRAfold)	0.678	0.550	0.259	0.495	0.505	0.154	0.426	0.413	0.066
(ViennaRNA)	0.669	0.500	0.144	0.480	0.461	0.091	0.212	0.317	0.041
ThreshKnot
(LinearPartition-C)	0.681	0.501	0.027	0.493	0.475	0.019	0.439	0.431	0.008
(LinearPartition-V)	0.669	0.484	0.033	0.481	0.456	0.026	0.383	0.372	0.014
Knotty	0.641	0.550	0.315	—	—	—	—	—	—
SPOT-RNA	0.658	0.621	0.322	0.462	0.479	0.127	—	—	—
CONTRAfold	0.682	0.519	0.000	0.500	0.497	0.000	0.425	0.415	0.000
RNAfold	0.668	0.472	0.000	0.474	0.442	0.000	0.361	0.347	0.000

Length	Short (12–150 nt)			Medium (151–500 nt)			Long (501–4381 nt)
	PKF	PK	CB	PKF	PK	CB	PKF	PK	CB
IPknot
(LinearPartition-C)	0.681	0.552	0.258	0.492	0.482	0.128	0.433	0.428	0.061
(LinearPartition-V)	0.669	0.499	0.143	0.478	0.461	0.091	0.380	0.370	0.038
(CONTRAfold)	0.678	0.550	0.259	0.495	0.505	0.154	0.426	0.413	0.066
(ViennaRNA)	0.669	0.500	0.144	0.480	0.461	0.091	0.212	0.317	0.041
ThreshKnot
(LinearPartition-C)	0.681	0.501	0.027	0.493	0.475	0.019	0.439	0.431	0.008
(LinearPartition-V)	0.669	0.484	0.033	0.481	0.456	0.026	0.383	0.372	0.014
Knotty	0.641	0.550	0.315	—	—	—	—	—	—
SPOT-RNA	0.658	0.621	0.322	0.462	0.479	0.127	—	—	—
CONTRAfold	0.682	0.519	0.000	0.500	0.497	0.000	0.425	0.415	0.000
RNAfold	0.668	0.472	0.000	0.474	0.442	0.000	0.361	0.347	0.000

PKF, |$F$|-value for pseudoknot-free sequences; PK, |$F$|-value for pseudoknotted sequences; CB, |$F$|-value of crossing base pairs.