CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		MCFold
MCC	0.527	>	0.432
Average MCC ± 95% Confidence Intervals	0.463 ± 0.170	>	0.376 ± 0.147
Sensitivity	0.375	<	0.454
Positive Predictive Value	0.748	>	0.421
Total TP	166	<	201
Total TN	53674	>	53418
Total FP	64	<	313
Total FP CONTRA	5	<	39
Total FP INCONS	51	<	238
Total FP COMP	8	<	36
Total FN	277	>	242
P-value	1.22797000563e-08

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

Total Scores
MCC	0.527
Average MCC ± 95% Confidence Intervals	0.463 ± 0.170
Sensitivity	0.375
Positive Predictive Value	0.748
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
2LKR_A	-	0.00	0.00	0.00	0	6101	4	0	4	0	39
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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
3U4M_B	-	0.58	0.43	0.80	16	3140	4	0	4	0	21
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
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

Total Scores
MCC	0.432
Average MCC ± 95% Confidence Intervals	0.376 ± 0.147
Sensitivity	0.454
Positive Predictive Value	0.421
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LA5_A	-	-0.03	0.00	0.00	0	615	15	0	15	0	19
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3J0L_2	-	0.21	0.24	0.18	8	6172	39	7	29	3	25
3J0L_g	-	0.13	0.25	0.08	1	452	12	8	4	0	3
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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