CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		ProbKnot
MCC	0.663	>	0.502
Average MCC ± 95% Confidence Intervals	0.642 ± 0.107	>	0.499 ± 0.103
Sensitivity	0.528	>	0.441
Positive Predictive Value	0.836	>	0.578
Total TP	387	>	323
Total TN	112841	>	112745
Total FP	98	<	285
Total FP CONTRA	0	<	28
Total FP INCONS	76	<	208
Total FP COMP	22	<	49
Total FN	346	<	410
P-value	5.06544643719e-08

Comparison of performance of PPfold(20) and ProbKnot. 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 PPfold(20) and ProbKnot).
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 PPfold(20) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and ProbKnot. 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 PPfold(20) and ProbKnot).

Total Scores
MCC	0.663
Average MCC ± 95% Confidence Intervals	0.642 ± 0.107
Sensitivity	0.528
Positive Predictive Value	0.836
Nr of predictions	20

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_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.78	0.62	0.97	33	7841	3	0	1	2	20
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.74	0.61	0.89	33	7103	4	0	4	0	21
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	13	0	10	3	30
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.68	0.94	34	7224	3	0	2	1	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.25	0.43	9	12225	18	0	12	6	27
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.21	0.52	11	14175	12	0	10	2	41
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	18	3467	1	0	1	0	14

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.499 ± 0.103
Sensitivity	0.441
Positive Predictive Value	0.578
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	7	0	6	1	7
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	0	9	2	27
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.35	0.63	19	7110	11	0	11	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7476	37	3	24	10	33
3J3F_7	5S_rRNA links to Rfam database...	0.76	0.64	0.91	32	7225	3	0	3	0	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.36	12	12213	35	3	18	14	24
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	16	14162	21	2	16	3	36
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	24	1	20	3	18
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22

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