CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		Alterna
MCC	0.696	>	0.608
Average MCC ± 95% Confidence Intervals	0.691 ± 0.116	>	0.638 ± 0.122
Sensitivity	0.533	<	0.544
Positive Predictive Value	0.915	>	0.690
Total TP	247	<	252
Total TN	32482	>	32387
Total FP	34	<	129
Total FP CONTRA	0	<	18
Total FP INCONS	23	<	95
Total FP COMP	11	<	16
Total FN	216	>	211
P-value	5.23657817852e-08

Total Scores
MCC	0.696
Average MCC ± 95% Confidence Intervals	0.691 ± 0.116
Sensitivity	0.533
Positive Predictive Value	0.915
Nr of predictions	29

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.72	0.53	1.00	8	457	0	0	0	0	7
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.20	0.04	1.00	1	2277	0	0	0	0	23
2YIE_X	-	0.76	0.58	1.00	7	1371	0	0	0	0	5
2YIE_Z	-	0.82	0.67	1.00	8	1532	0	0	0	0	4
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	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	1	0	0	1	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...	0.72	0.54	0.95	20	3549	1	0	1	0	17

Total Scores
MCC	0.608
Average MCC ± 95% Confidence Intervals	0.638 ± 0.122
Sensitivity	0.544
Positive Predictive Value	0.690
Nr of predictions	29

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
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
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
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_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_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3NMU_E	-	-0.01	0.00	0.00	0	553	10	2	6	2	6
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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

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