CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		RNAwolf
MCC	0.684	>	0.678
Average MCC ± 95% Confidence Intervals	0.695 ± 0.147	>	0.652 ± 0.174
Sensitivity	0.705	>	0.674
Positive Predictive Value	0.679	<	0.698
Total TP	186	>	178
Total TN	10300	<	10319
Total FP	115	>	104
Total FP CONTRA	27	>	15
Total FP INCONS	61	<	62
Total FP COMP	27	=	27
Total FN	78	<	86
P-value	0.00781880629872

Comparison of performance of Alterna and RNAwolf. 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 Alterna and RNAwolf).
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 Alterna and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and RNAwolf. 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 Alterna and RNAwolf).

Total Scores
MCC	0.684
Average MCC ± 95% Confidence Intervals	0.695 ± 0.147
Sensitivity	0.705
Positive Predictive Value	0.679
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.44	0.53	8	513	7	0	7	0	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	9	1	3	5	3
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.63	0.62	0.67	8	472	8	0	4	4	5
3J0L_7	-	0.37	0.40	0.36	4	508	9	2	5	2	6
3J0L_g	-	-0.02	0.00	0.00	0	169	9	3	4	2	2
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3RKF_A	Purine links to Rfam database...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13
3SIU_F	-	0.69	0.75	0.67	6	136	3	0	3	0	2
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.68	0.75	0.63	12	1274	13	4	3	6	4

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.652 ± 0.174
Sensitivity	0.674
Positive Predictive Value	0.698
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	9	512	7	0	7	0	9
2LDL_A	-	0.88	0.78	1.00	7	133	0	0	0	0	2
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	0.62	0.63	0.63	5	594	7	1	2	4	3
2YIE_X	-	-0.01	0.00	0.00	0	536	11	1	7	3	7
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_7	-	-0.02	0.00	0.00	0	509	10	1	9	0	10
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	1	9
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	103	6	0	5	1	5
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2

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