CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Sfold		RNASLOpt
MCC	0.480	>	0.443
Average MCC ± 95% Confidence Intervals	0.427 ± 0.152	>	0.409 ± 0.141
Sensitivity	0.393	>	0.365
Positive Predictive Value	0.595	>	0.547
Total TP	157	>	146
Total TN	51813	>	51810
Total FP	120	<	130
Total FP CONTRA	13	<	15
Total FP INCONS	94	<	106
Total FP COMP	13	>	9
Total FN	243	<	254
P-value	2.8150742666e-08

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

Total Scores
MCC	0.480
Average MCC ± 95% Confidence Intervals	0.427 ± 0.152
Sensitivity	0.393
Positive Predictive Value	0.595
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	0	5	0	13
2LKR_A	-	0.89	0.79	1.00	31	6074	1	0	0	1	8
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J0L_2	-	0.36	0.33	0.39	11	6188	19	2	15	2	22
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
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...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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.