CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		Pknots
MCC	0.729	>	0.676
Average MCC ± 95% Confidence Intervals	0.716 ± 0.103	>	0.678 ± 0.115
Sensitivity	0.719	>	0.693
Positive Predictive Value	0.747	>	0.668
Total TP	422	>	407
Total TN	37421	>	37377
Total FP	178	<	248
Total FP CONTRA	51	<	65
Total FP INCONS	92	<	137
Total FP COMP	35	<	46
Total FN	165	<	180
P-value	5.1503931209e-08

Comparison of performance of Contrafold and Pknots. 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 Contrafold and Pknots).
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 Contrafold and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and Pknots. 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 Contrafold and Pknots).

Total Scores
MCC	0.729
Average MCC ± 95% Confidence Intervals	0.716 ± 0.103
Sensitivity	0.719
Positive Predictive Value	0.747
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.71	0.63	0.83	5	230	1	1	0	0	3
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
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	-	0.76	0.71	0.83	5	152	1	1	0	0	2
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
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...	0.86	0.79	0.96	22	1449	1	0	1	0	6
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3NPB_A	SAM links to Rfam database...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
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...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

Total Scores
MCC	0.676
Average MCC ± 95% Confidence Intervals	0.678 ± 0.115
Sensitivity	0.693
Positive Predictive Value	0.668
Nr of predictions	26

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.17	0.25	0.17	2	224	10	3	7	0	6
2KRL_A	-	0.79	0.83	0.76	19	1999	13	5	1	7	4
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
2RP0_A	-	0.87	1.00	0.78	7	107	2	2	0	0	0
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.50	0.55	0.48	12	1083	13	3	10	0	10
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	-	0.66	0.57	0.80	4	153	3	0	1	2	3
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3IWN_A	c-di-GMP-I links to Rfam database...	0.22	0.21	0.25	6	1448	18	2	16	0	22
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NKB_B	-	0.64	0.68	0.62	13	714	8	0	8	0	6
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
3U4M_B	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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