CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MaxExpect		RNAsubopt
MCC	0.623	>	0.579
Average MCC ± 95% Confidence Intervals	0.628 ± 0.119	>	0.573 ± 0.127
Sensitivity	0.640	>	0.608
Positive Predictive Value	0.612	>	0.558
Total TP	422	>	401
Total TN	82278	>	82250
Total FP	337	<	386
Total FP CONTRA	99	<	122
Total FP INCONS	169	<	195
Total FP COMP	69	=	69
Total FN	237	<	258
P-value	5.1503931209e-08

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

Total Scores
MCC	0.623
Average MCC ± 95% Confidence Intervals	0.628 ± 0.119
Sensitivity	0.640
Positive Predictive Value	0.612
Nr of predictions	23

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
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	0.579
Average MCC ± 95% Confidence Intervals	0.573 ± 0.127
Sensitivity	0.608
Positive Predictive Value	0.558
Nr of predictions	23

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.62	0.61	0.64	14	2002	15	5	3	7	9
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	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22342	96	41	37	18	31
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.53	57	25429	54	26	24	4	38
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3NPB_A	SAM links to Rfam database...	0.84	0.78	0.91	29	2246	8	0	3	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
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...	0.36	0.33	0.42	5	484	7	0	7	0	10

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