CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		McQFold
MCC	0.711	>	0.613
Average MCC ± 95% Confidence Intervals	0.691 ± 0.117	>	0.683 ± 0.155
Sensitivity	0.663	>	0.640
Positive Predictive Value	0.768	>	0.593
Total TP	381	>	368
Total TN	77219	>	77094
Total FP	184	<	289
Total FP CONTRA	60	<	103
Total FP INCONS	55	<	150
Total FP COMP	69	>	36
Total FN	194	<	207
P-value	3.60448791174e-08

Comparison of performance of MXScarna(seed) and McQFold. 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 MXScarna(seed) and McQFold).
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 MXScarna(seed) and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and McQFold. 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 MXScarna(seed) and McQFold).

Total Scores
MCC	0.711
Average MCC ± 95% Confidence Intervals	0.691 ± 0.117
Sensitivity	0.663
Positive Predictive Value	0.768
Nr of predictions	19

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	518	12	0	10	2	18
2ZZN_D	tRNA links to Rfam database...	0.95	0.91	1.00	20	964	0	0	0	0	2
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.77	0.92	23	1475	4	0	2	2	7
3GX2_A	SAM links to Rfam database...	0.83	0.82	0.85	23	1422	7	2	2	3	5
3IVN_B	Purine links to Rfam database...	0.69	0.57	0.87	13	888	2	2	0	0	10
3IYQ_A	tmRNA links to Rfam database...	0.44	0.47	0.41	24	22382	49	21	13	15	27
3IZ4_A	tmRNA links to Rfam database...	0.73	0.64	0.82	61	25462	22	12	1	9	34
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3LA5_A	Purine links to Rfam database...	0.82	0.72	0.95	18	935	1	1	0	0	7
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	26	2247	10	2	3	5	11
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	20	5	3	12	11
3PDR_A	ykoK links to Rfam database...	0.87	0.88	0.86	44	4789	10	4	3	3	6
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	4	4	1	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

Total Scores
MCC	0.613
Average MCC ± 95% Confidence Intervals	0.683 ± 0.155
Sensitivity	0.640
Positive Predictive Value	0.593
Nr of predictions	19

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...	0.64	0.61	0.69	11	512	5	1	4	0	7
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.22	0.31	0.15	16	22335	100	45	44	11	35
3IZ4_A	tmRNA links to Rfam database...	0.46	0.46	0.47	44	25442	56	14	36	6	51
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.90	0.81	1.00	30	2248	5	0	0	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
3PDR_A	ykoK links to Rfam database...	0.83	0.80	0.87	40	4794	9	2	4	3	10
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...	0.82	0.83	0.83	24	1504	5	1	4	0	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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