CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RNASLOpt
MCC	0.466	>	0.454
Average MCC ± 95% Confidence Intervals	0.496 ± 0.100	>	0.431 ± 0.115
Sensitivity	0.390	>	0.373
Positive Predictive Value	0.565	>	0.559
Total TP	305	>	292
Total TN	104698	<	104716
Total FP	248	>	242
Total FP CONTRA	20	>	19
Total FP INCONS	215	>	211
Total FP COMP	13	>	12
Total FN	477	<	490
P-value	1.24386558293e-07

Comparison of performance of Cylofold 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 Cylofold and RNASLOpt).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for Cylofold and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold 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 Cylofold and RNASLOpt).

Total Scores
MCC	0.466
Average MCC ± 95% Confidence Intervals	0.496 ± 0.100
Sensitivity	0.390
Positive Predictive Value	0.565
Nr of predictions	25

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	5	0	5	0	9
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
2M58_A	-	0.51	0.41	0.64	7	1642	4	1	3	0	10
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.69	0.70	0.70	16	2903	7	2	5	0	7
3J2C_O	-	0.43	0.33	0.55	21	10258	18	0	17	1	42
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25
3ZEX_E	-	0.00	0.00	0.00	0	21897	51	2	46	3	77
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.49	0.69	24	6986	11	0	11	0	25
3ZND_W	tRNA links to Rfam database...	0.40	0.39	0.41	9	2981	15	2	11	2	14
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.73	0.70	0.78	7	519	2	1	1	0	3
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	0.70	0.50	1.00	8	587	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.14	0.31	5	5135	11	2	9	0	31

Total Scores
MCC	0.454
Average MCC ± 95% Confidence Intervals	0.431 ± 0.115
Sensitivity	0.373
Positive Predictive Value	0.559
Nr of predictions	25

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
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2C_O	-	0.62	0.49	0.78	31	10256	10	0	9	1	32
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
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
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	4	49	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.59	0.97	29	6991	1	0	1	0	20
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.22	5	2980	20	1	17	2	18
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
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
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FNJ_A	-	-0.02	0.00	0.00	0	584	11	0	11	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.17	0.26	6	5128	17	2	15	0	30

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