CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MaxExpect		UNAFold
MCC	0.648	>	0.554
Average MCC ± 95% Confidence Intervals	0.630 ± 0.113	>	0.618 ± 0.117
Sensitivity	0.660	>	0.575
Positive Predictive Value	0.637	>	0.535
Total TP	953	>	831
Total TN	1567351	>	1567294
Total FP	673	<	845
Total FP CONTRA	180	<	187
Total FP INCONS	364	<	536
Total FP COMP	129	>	122
Total FN	492	<	614
P-value	5.06544643719e-08

Comparison of performance of MaxExpect and UNAFold. 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 MaxExpect and UNAFold).
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 MaxExpect and UNAFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for MaxExpect and UNAFold. 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 MaxExpect and UNAFold).

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.630 ± 0.113
Sensitivity	0.660
Positive Predictive Value	0.637
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22342	96	41	40	15	34
3IZ4_A	tmRNA links to Rfam database...	0.61	0.61	0.62	58	25442	42	14	22	6	37
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3JYV_7	tRNA links to Rfam database...	0.48	0.45	0.53	9	1094	9	3	5	1	11
3KIY_A	-	0.67	0.68	0.66	531	1485073	336	81	195	60	255
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	10	0	6	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	11
3PDR_A	ykoK links to Rfam database...	0.92	0.90	0.94	45	4792	5	1	2	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

Total Scores
MCC	0.554
Average MCC ± 95% Confidence Intervals	0.618 ± 0.117
Sensitivity	0.575
Positive Predictive Value	0.535
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	96	46	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.58	0.60	0.57	57	25436	53	12	31	10	38
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3JYV_7	tRNA links to Rfam database...	0.24	0.25	0.25	5	1091	16	7	8	1	15
3KIY_A	-	0.50	0.52	0.48	410	1485034	486	79	357	50	376
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	34	5	15	14	11
3PDR_A	ykoK links to Rfam database...	0.93	0.92	0.94	46	4791	5	1	2	2	4
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	11	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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