CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAsubopt		Afold
MCC	0.569	>	0.543
Average MCC ± 95% Confidence Intervals	0.566 ± 0.132	>	0.534 ± 0.127
Sensitivity	0.603	>	0.581
Positive Predictive Value	0.544	>	0.514
Total TP	381	>	367
Total TN	79188	>	79175
Total FP	390	<	422
Total FP CONTRA	118	<	122
Total FP INCONS	202	<	225
Total FP COMP	70	<	75
Total FN	251	<	265
P-value	5.23657817852e-08

Comparison of performance of RNAsubopt and Afold. 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 RNAsubopt and Afold).
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 RNAsubopt and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAsubopt and Afold. 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 RNAsubopt and Afold).

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.566 ± 0.132
Sensitivity	0.603
Positive Predictive Value	0.544
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.52	0.55	0.52	12	961	11	3	8	0	10
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22342	96	41	37	18	31
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.53	57	25429	54	26	24	4	38
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.33	0.20	5	2717	32	7	13	12	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3NPB_A	SAM links to Rfam database...	0.84	0.78	0.91	29	2246	8	0	3	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.94	0.97	31	1957	2	0	1	1	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

Total Scores
MCC	0.543
Average MCC ± 95% Confidence Intervals	0.534 ± 0.127
Sensitivity	0.581
Positive Predictive Value	0.514
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	228	8	1	7	0	8
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
2RP0_A	-	0.76	0.71	0.83	5	110	1	0	1	0	2
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3GCA_A	-	-0.04	0.00	0.00	0	151	9	1	6	2	7
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.67	0.68	0.68	19	1444	9	1	8	0	9
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4JRC_A	-	0.27	0.29	0.29	5	605	12	0	12	0	12

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