CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(20)		RNAwolf
MCC	0.716	>	0.438
Average MCC ± 95% Confidence Intervals	0.708 ± 0.108	>	0.460 ± 0.117
Sensitivity	0.666	>	0.454
Positive Predictive Value	0.776	>	0.434
Total TP	339	>	231
Total TN	45519	>	45424
Total FP	158	<	374
Total FP CONTRA	28	<	77
Total FP INCONS	70	<	224
Total FP COMP	60	<	73
Total FN	170	<	278
P-value	5.19332990918e-08

Comparison of performance of RNASampler(20) and RNAwolf. 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 RNASampler(20) and RNAwolf).
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 RNASampler(20) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and RNAwolf. 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 RNASampler(20) and RNAwolf).

Total Scores
MCC	0.716
Average MCC ± 95% Confidence Intervals	0.708 ± 0.108
Sensitivity	0.666
Positive Predictive Value	0.776
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
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...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	21	5	8	8	12
3J3E_7	5S_rRNA links to Rfam database...	0.80	0.76	0.84	26	2710	6	0	5	1	8
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.47	0.39	9	4738	20	6	8	6	10
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.72	0.84	26	2903	5	0	5	0	10
3J3V_B	5S_rRNA links to Rfam database...	0.88	0.78	1.00	21	2635	4	0	0	4	6
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...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZND_W	tRNA links to Rfam database...	0.58	0.75	0.46	6	1178	18	4	3	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

Total Scores
MCC	0.438
Average MCC ± 95% Confidence Intervals	0.460 ± 0.117
Sensitivity	0.454
Positive Predictive Value	0.434
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J20_1	tRNA links to Rfam database...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12

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