CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		IPknot
MCC	0.669	>	0.526
Average MCC ± 95% Confidence Intervals	0.645 ± 0.104	>	0.529 ± 0.105
Sensitivity	0.511	>	0.433
Positive Predictive Value	0.880	>	0.645
Total TP	404	>	342
Total TN	119866	>	119795
Total FP	67	<	223
Total FP CONTRA	4	<	16
Total FP INCONS	51	<	172
Total FP COMP	12	<	35
Total FN	386	<	448
P-value	5.10776592382e-08

Comparison of performance of CentroidAlifold(20) and IPknot. 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 CentroidAlifold(20) and IPknot).
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 CentroidAlifold(20) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and IPknot. 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 CentroidAlifold(20) and IPknot).

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.645 ± 0.104
Sensitivity	0.511
Positive Predictive Value	0.880
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...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.76	0.58	1.00	31	7844	2	0	0	2	22
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7499	4	0	4	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	10	0	10	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.25	0.60	9	12231	6	1	5	0	27
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.66	0.47	0.93	27	6992	2	0	2	0	30
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.21	0.69	11	14180	5	1	4	0	41
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.53	0.89	17	3467	2	1	1	0	15

Total Scores
MCC	0.526
Average MCC ± 95% Confidence Intervals	0.529 ± 0.105
Sensitivity	0.433
Positive Predictive Value	0.645
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...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.66	0.55	0.81	29	7839	9	0	7	2	24
3J3D_C	tRNA links to Rfam database...	0.52	0.43	0.63	12	2756	7	0	7	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7484	25	2	17	6	33
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.35	0.63	19	7110	11	0	11	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	37	4	20	13	24
3J3F_7	5S_rRNA links to Rfam database...	0.67	0.60	0.75	30	7220	10	1	9	0	20
3J3V_B	5S_rRNA links to Rfam database...	0.40	0.30	0.55	17	6990	14	0	14	0	40
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.63	0.82	31	6983	7	0	7	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.21	0.79	11	14182	6	1	2	3	41
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.52	0.42	0.67	8	1314	4	0	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.56	0.86	18	3465	3	1	2	0	14

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