CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		CentroidHomfold‑LAST
MCC	0.599	>	0.584
Average MCC ± 95% Confidence Intervals	0.576 ± 0.091	<	0.589 ± 0.107
Sensitivity	0.451	<	0.491
Positive Predictive Value	0.800	>	0.700
Total TP	333	<	362
Total TN	105713	>	105612
Total FP	102	<	183
Total FP CONTRA	5	<	18
Total FP INCONS	78	<	137
Total FP COMP	19	<	28
Total FN	405	>	376
P-value	2.40326410557e-07

Comparison of performance of Murlet(20) and CentroidHomfold-LAST. 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 Murlet(20) and CentroidHomfold‑LAST).
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 Murlet(20) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and CentroidHomfold-LAST. 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 Murlet(20) and CentroidHomfold‑LAST).

Total Scores
MCC	0.599
Average MCC ± 95% Confidence Intervals	0.576 ± 0.091
Sensitivity	0.451
Positive Predictive Value	0.800
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...	0.77	0.67	0.90	18	2983	3	0	2	1	9
3J20_0	tRNA links to Rfam database...	0.58	0.47	0.74	14	2831	5	0	5	0	16
3J20_1	tRNA links to Rfam database...	0.68	0.57	0.81	13	2910	3	0	3	0	10
3J2L_3	5S_rRNA links to Rfam database...	0.69	0.49	0.96	26	7848	3	0	1	2	27
3J3D_C	tRNA links to Rfam database...	0.78	0.64	0.95	18	2756	1	0	1	0	10
3J3E_8	5_8S_rRNA links to Rfam database...	0.24	0.15	0.38	5	7490	13	1	7	5	28
3J3E_7	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.36	0.65	13	12226	10	0	7	3	23
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.50	0.96	25	7234	1	0	1	0	25
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.40	1.00	23	6998	0	0	0	0	34
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	22	7114	4	0	4	0	32
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.20	5	11756	24	2	18	4	28
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	4	3470	12	1	11	0	28

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.589 ± 0.107
Sensitivity	0.491
Positive Predictive Value	0.700
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...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J20_0	tRNA links to Rfam database...	0.35	0.37	0.34	11	2818	22	3	18	1	19
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...	0.73	0.62	0.87	33	7837	7	0	5	2	20
3J3D_C	tRNA links to Rfam database...	0.68	0.61	0.77	17	2753	5	0	5	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.05	0.03	0.08	1	7490	16	1	11	4	32
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.54	0.76	29	7102	9	0	9	0	25
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	33	4	20	9	24
3J3F_7	5S_rRNA links to Rfam database...	0.65	0.58	0.74	29	7221	10	1	9	0	21
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.37	0.72	21	6992	8	1	7	0	36
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...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	0	5	0	17
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
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...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.41	0.43	13	3456	17	3	14	0	19

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