CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		ProbKnot
MCC	0.812	>	0.670
Average MCC ± 95% Confidence Intervals	0.784 ± 0.124	>	0.673 ± 0.124
Sensitivity	0.753	>	0.686
Positive Predictive Value	0.880	>	0.662
Total TP	278	>	253
Total TN	28004	>	27938
Total FP	59	<	172
Total FP CONTRA	4	<	39
Total FP INCONS	34	<	90
Total FP COMP	21	<	43
Total FN	91	<	116
P-value	1.06761512825e-08

Comparison of performance of PPfold(20) and ProbKnot. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for PPfold(20) and ProbKnot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PPfold(20) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and ProbKnot. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for PPfold(20) and ProbKnot).

Total Scores
MCC	0.812
Average MCC ± 95% Confidence Intervals	0.784 ± 0.124
Sensitivity	0.753
Positive Predictive Value	0.880
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.66	0.50	0.90	9	347	1	0	1	0	9
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	4	0	0	4	2
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	9	5355	14	0	10	4	20
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	6	0	2	4	3
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	2	0	2	0	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.75	0.95	18	1183	1	0	1	0	6

Total Scores
MCC	0.670
Average MCC ± 95% Confidence Intervals	0.673 ± 0.124
Sensitivity	0.686
Positive Predictive Value	0.662
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.76	0.81	26	2988	11	0	6	5	8
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.52	0.45	15	5341	22	4	14	4	14
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	7	0	2	5	5
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.38	0.38	0.41	9	1180	13	6	7	0	15

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.