CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		RNASLOpt
MCC	0.601	>	0.567
Average MCC ± 95% Confidence Intervals	0.664 ± 0.192	>	0.627 ± 0.206
Sensitivity	0.537	>	0.458
Positive Predictive Value	0.684	<	0.713
Total TP	108	>	92
Total TN	13732	<	13761
Total FP	56	>	43
Total FP CONTRA	8	>	2
Total FP INCONS	42	>	35
Total FP COMP	6	=	6
Total FN	93	<	109
P-value	1.61358433984e-08

Comparison of performance of Alterna and RNASLOpt. 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 Alterna and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and RNASLOpt. 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 Alterna and RNASLOpt).

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.664 ± 0.192
Sensitivity	0.537
Positive Predictive Value	0.684
Nr of predictions	14

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...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_1	-	0.61	0.53	0.71	10	1211	6	0	4	2	9
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.627 ± 0.206
Sensitivity	0.458
Positive Predictive Value	0.713
Nr of predictions	14

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.48	0.32	0.71	12	3553	5	0	5	0	25

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