CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		RNASLOpt
MCC	0.517	>	0.443
Average MCC ± 95% Confidence Intervals	0.464 ± 0.158	>	0.409 ± 0.141
Sensitivity	0.438	>	0.365
Positive Predictive Value	0.618	>	0.547
Total TP	175	>	146
Total TN	51794	<	51810
Total FP	124	<	130
Total FP CONTRA	15	=	15
Total FP INCONS	93	<	106
Total FP COMP	16	>	9
Total FN	225	<	254
P-value	5.52090997893e-09

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

Total Scores
MCC	0.517
Average MCC ± 95% Confidence Intervals	0.464 ± 0.158
Sensitivity	0.438
Positive Predictive Value	0.618
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...	0.45	0.35	0.58	7	1528	5	2	3	0	13
2LKR_A	-	0.84	0.79	0.89	31	6070	6	0	4	2	8
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_2	-	0.25	0.24	0.28	8	6187	26	0	21	5	25
3J0L_g	-	0.00	0.00	0.00	0	464	1	1	0	0	4
3J0L_a	-	0.50	0.44	0.58	7	1116	5	2	3	0	9
3J16_L	tRNA links to Rfam database...	0.46	0.40	0.55	12	2753	10	1	9	0	18
3U4M_B	-	0.59	0.46	0.77	17	3138	5	0	5	0	20
3UZL_B	tRNA links to Rfam database...	0.70	0.54	0.91	20	3548	2	0	2	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8

Total Scores
MCC	0.443
Average MCC ± 95% Confidence Intervals	0.409 ± 0.141
Sensitivity	0.365
Positive Predictive Value	0.547
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
2LKR_A	-	0.68	0.62	0.75	24	6073	9	0	8	1	15
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
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
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.32	0.71	12	3553	5	0	5	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
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...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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