CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		RNAwolf
MCC	0.589	>	0.584
Average MCC ± 95% Confidence Intervals	0.631 ± 0.142	>	0.597 ± 0.155
Sensitivity	0.527	<	0.543
Positive Predictive Value	0.669	>	0.639
Total TP	194	<	200
Total TN	26987	>	26964
Total FP	107	<	125
Total FP CONTRA	15	>	13
Total FP INCONS	81	<	100
Total FP COMP	11	<	12
Total FN	174	>	168
P-value	0.00321277492933

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	0.589
Average MCC ± 95% Confidence Intervals	0.631 ± 0.142
Sensitivity	0.527
Positive Predictive Value	0.669
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	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2YIE_X	-	0.36	0.33	0.40	4	1368	9	2	4	3	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_1	-	0.61	0.53	0.71	10	1211	6	0	4	2	9
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26
3SIU_F	-	0.59	0.55	0.67	6	369	3	0	3	0	5
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.597 ± 0.155
Sensitivity	0.543
Positive Predictive Value	0.639
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	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LDL_A	-	0.74	0.64	0.88	7	343	1	0	1	0	4
2LDT_A	-	0.86	0.80	0.92	12	452	1	0	1	0	3
2LK3_A	-	1.00	1.00	1.00	10	266	0	0	0	0	0
2YIE_X	-	-0.01	0.00	0.00	0	1364	15	4	10	1	12
2YIE_Z	-	0.43	0.42	0.45	5	1529	9	1	5	3	7
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_1	-	0.68	0.63	0.75	12	1209	5	0	4	1	7
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3TRZ_Z	-	0.91	0.83	1.00	5	205	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	2	0	0	2	0
3TS2_V	-	-0.02	0.00	0.00	0	270	7	0	6	1	5
3UZL_B	tRNA links to Rfam database...	0.72	0.59	0.88	22	3545	4	1	2	1	15

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