CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		CRWrnafold
MCC	0.531	>	0.467
Average MCC ± 95% Confidence Intervals	0.462 ± 0.182	>	0.424 ± 0.161
Sensitivity	0.380	<	0.410
Positive Predictive Value	0.749	>	0.540
Total TP	164	<	177
Total TN	55207	>	55098
Total FP	64	<	167
Total FP CONTRA	5	<	18
Total FP INCONS	50	<	133
Total FP COMP	9	<	16
Total FN	268	>	255
P-value	2.32677072069e-08

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

Total Scores
MCC	0.531
Average MCC ± 95% Confidence Intervals	0.462 ± 0.182
Sensitivity	0.380
Positive Predictive Value	0.749
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
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

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.424 ± 0.161
Sensitivity	0.410
Positive Predictive Value	0.540
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.52	0.44	0.63	17	6078	12	2	8	2	22
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	1	4	0	11
3J0L_2	-	0.25	0.24	0.28	8	6187	23	2	19	2	25
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J16_L	tRNA links to Rfam database...	0.84	0.70	1.00	21	2754	0	0	0	0	9
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

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