CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		Vsfold4
MCC	0.546	>	0.486
Average MCC ± 95% Confidence Intervals	0.519 ± 0.119	>	0.492 ± 0.114
Sensitivity	0.590	>	0.493
Positive Predictive Value	0.511	>	0.487
Total TP	396	>	331
Total TN	88726	<	88821
Total FP	489	>	425
Total FP CONTRA	151	>	121
Total FP INCONS	228	=	228
Total FP COMP	110	>	76
Total FN	275	<	340
P-value	5.23657817852e-08

Comparison of performance of ProbKnot and Vsfold4. 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 ProbKnot and Vsfold4).
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 ProbKnot and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and Vsfold4. 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 ProbKnot and Vsfold4).

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.519 ± 0.119
Sensitivity	0.590
Positive Predictive Value	0.511
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.82	0.87	0.77	20	1998	15	6	0	9	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2M58_A	-	-0.02	0.00	0.00	0	529	15	0	15	0	12
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22346	97	41	36	20	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J3D_C	tRNA links to Rfam database...	0.46	0.53	0.42	10	944	14	6	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	37	6	18	13	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.33	9	4734	38	9	9	20	10
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
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
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
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
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
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
4JF2_A	preQ1-II links to Rfam database...	0.91	0.92	0.92	22	1058	2	2	0	0	2
4JRC_A	-	0.28	0.29	0.31	5	606	11	0	11	0	12

Total Scores
MCC	0.486
Average MCC ± 95% Confidence Intervals	0.492 ± 0.114
Sensitivity	0.493
Positive Predictive Value	0.487
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.84	0.83	0.86	19	2002	9	2	1	6	4
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2M58_A	-	-0.02	0.00	0.00	0	538	6	0	6	0	12
3IYQ_A	tmRNA links to Rfam database...	0.27	0.35	0.21	18	22353	80	40	29	11	33
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.23	0.24	0.24	7	1504	22	5	17	0	22
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4JF2_A	preQ1-II links to Rfam database...	0.74	0.67	0.84	16	1063	3	0	3	0	8
4JRC_A	-	0.34	0.29	0.42	5	610	7	0	7	0	12

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