CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(20)		RNAwolf
MCC	0.585	>	0.348
Average MCC ± 95% Confidence Intervals	0.595 ± 0.100	>	0.375 ± 0.099
Sensitivity	0.448	>	0.328
Positive Predictive Value	0.768	>	0.379
Total TP	354	>	259
Total TN	119864	>	119641
Total FP	143	<	467
Total FP CONTRA	7	<	53
Total FP INCONS	100	<	372
Total FP COMP	36	<	42
Total FN	436	<	531
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	0.585
Average MCC ± 95% Confidence Intervals	0.595 ± 0.100
Sensitivity	0.448
Positive Predictive Value	0.768
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...	0.82	0.70	0.95	19	2983	3	0	1	2	8
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...	0.80	0.67	0.95	20	2829	2	0	1	1	10
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	12	1	9	2	36
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...	0.12	0.09	0.18	3	7486	21	2	12	7	30
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.48	0.81	26	7108	6	0	6	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.33	0.46	12	12220	17	1	13	3	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	5	0	5	0	24
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.42	0.96	24	6996	1	0	1	0	33
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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.49	0.96	24	6996	1	0	1	0	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.19	0.38	10	14170	20	1	15	4	42
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	15	2	10	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.41	0.76	13	3469	4	0	4	0	19

Total Scores
MCC	0.348
Average MCC ± 95% Confidence Intervals	0.375 ± 0.099
Sensitivity	0.328
Positive Predictive Value	0.379
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...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J20_1	tRNA links to Rfam database...	0.46	0.52	0.41	12	2897	17	6	11	0	11
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.55	0.49	0.62	26	7833	18	0	16	2	27
3J3D_C	tRNA links to Rfam database...	0.79	0.75	0.84	21	2750	5	2	2	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.20	0.23	10	7216	34	2	32	0	40
3J3V_B	5S_rRNA links to Rfam database...	0.43	0.37	0.51	21	6980	20	2	18	0	36
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.05	0.06	0.06	3	14144	49	12	37	0	49
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.50	0.64	16	3461	10	1	8	1	16

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