CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		Afold
MCC	0.393	>	0.383
Average MCC ± 95% Confidence Intervals	0.371 ± 0.165	<	0.383 ± 0.150
Sensitivity	0.331	<	0.344
Positive Predictive Value	0.474	>	0.434
Total TP	180	<	187
Total TN	92213	>	92162
Total FP	221	<	277
Total FP CONTRA	20	<	23
Total FP INCONS	180	<	221
Total FP COMP	21	<	33
Total FN	363	>	356
P-value	5.26278708866e-06

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

Total Scores
MCC	0.393
Average MCC ± 95% Confidence Intervals	0.371 ± 0.165
Sensitivity	0.331
Positive Predictive Value	0.474
Nr of predictions	17

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
2M58_A	-	0.32	0.24	0.44	4	1644	5	1	4	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J2C_O	-	0.62	0.49	0.78	31	10256	10	0	9	1	32
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	30	1	19	10	33
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.59	0.97	29	6991	1	0	1	0	20
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	4	49	2	77
3ZEX_H	-	0.19	0.18	0.21	7	9012	26	4	22	0	31
3ZEX_F	-	0.00	0.00	0.00	0	2628	0	0	0	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4FNJ_A	-	-0.02	0.00	0.00	0	584	11	0	11	0	16
4JRC_A	-	0.83	0.70	1.00	16	1524	0	0	0	0	7

Total Scores
MCC	0.383
Average MCC ± 95% Confidence Intervals	0.383 ± 0.150
Sensitivity	0.344
Positive Predictive Value	0.434
Nr of predictions	17

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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.33	0.29	0.38	5	1640	8	1	7	0	12
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J2C_O	-	0.58	0.49	0.69	31	10251	15	1	13	1	32
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	31	2	19	10	28
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	2	51	2	77
3ZEX_H	-	0.18	0.18	0.18	7	9006	33	6	26	1	31
3ZEX_F	-	0.00	0.00	0.00	0	2617	12	2	9	1	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ATO_G	-	0.32	0.30	0.38	3	520	6	1	4	1	7
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8
4FNJ_A	-	0.75	0.63	0.91	10	584	1	0	1	0	6
4JRC_A	-	0.24	0.22	0.29	5	1523	12	0	12	0	18

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