CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		MaxExpect
MCC	0.558	>	0.506
Average MCC ± 95% Confidence Intervals	0.547 ± 0.139	>	0.465 ± 0.138
Sensitivity	0.555	>	0.509
Positive Predictive Value	0.572	>	0.516
Total TP	227	>	208
Total TN	32988	>	32982
Total FP	227	<	254
Total FP CONTRA	73	>	60
Total FP INCONS	97	<	135
Total FP COMP	57	<	59
Total FN	182	<	201
P-value	5.23657817852e-08

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

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.547 ± 0.139
Sensitivity	0.555
Positive Predictive Value	0.572
Nr of predictions	20

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
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...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.465 ± 0.138
Sensitivity	0.509
Positive Predictive Value	0.516
Nr of predictions	20

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2M58_A	-	-0.02	0.00	0.00	0	531	13	0	13	0	12
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	2	10	1	9
3J3D_C	tRNA links to Rfam database...	0.47	0.53	0.43	10	945	13	5	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2719	32	5	16	11	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.42	0.29	8	4733	39	10	10	19	11
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.97	0.94	1.00	31	1958	1	0	0	1	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.54	0.45	0.65	13	5354	17	2	5	10	16
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
4ATO_G	-	0.45	0.43	0.50	3	214	3	3	0	0	4
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.29	0.25	0.35	6	1185	11	4	7	0	18
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.46	0.57	13	1825	10	5	5	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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