CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(20)		RNAshapes
MCC	0.753	>	0.637
Average MCC ± 95% Confidence Intervals	0.747 ± 0.122	>	0.631 ± 0.162
Sensitivity	0.656	>	0.637
Positive Predictive Value	0.869	>	0.644
Total TP	298	>	289
Total TN	51920	>	51814
Total FP	66	<	208
Total FP CONTRA	18	<	50
Total FP INCONS	27	<	110
Total FP COMP	21	<	48
Total FN	156	<	165
P-value	1.87872347734e-08

Comparison of performance of RNAalifold(20) and RNAshapes. 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 RNAalifold(20) and RNAshapes).
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 RNAalifold(20) and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and RNAshapes. 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 RNAalifold(20) and RNAshapes).

Total Scores
MCC	0.753
Average MCC ± 95% Confidence Intervals	0.747 ± 0.122
Sensitivity	0.656
Positive Predictive Value	0.869
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.78	0.95	18	884	1	1	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3LA5_A	Purine links to Rfam database...	0.87	0.76	1.00	19	935	0	0	0	0	6
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.631 ± 0.162
Sensitivity	0.637
Positive Predictive Value	0.644
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3GX2_A	SAM links to Rfam database...	0.91	0.89	0.93	25	1422	3	1	1	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.56	55	25437	50	16	28	6	40
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.84	0.76	0.93	28	2248	5	1	1	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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