CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Sfold		Mastr(20)
MCC	0.665	>	0.506
Average MCC ± 95% Confidence Intervals	0.656 ± 0.154	>	0.489 ± 0.199
Sensitivity	0.628	>	0.337
Positive Predictive Value	0.711	<	0.769
Total TP	285	>	153
Total TN	51862	<	52064
Total FP	148	>	52
Total FP CONTRA	38	>	10
Total FP INCONS	78	>	36
Total FP COMP	32	>	6
Total FN	169	<	301
P-value	2.76499031155e-08

Comparison of performance of Sfold and Mastr(20). 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 Sfold and Mastr(20)).
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 Sfold and Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and Mastr(20). 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 Sfold and Mastr(20)).

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.656 ± 0.154
Sensitivity	0.628
Positive Predictive Value	0.711
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...	0.86	0.79	0.96	22	1426	2	1	0	1	6
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...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1095	16	2	14	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...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
3PDR_A	ykoK links to Rfam database...	0.82	0.80	0.85	40	4793	9	2	5	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...	0.78	0.72	0.84	21	1508	4	2	2	0	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.489 ± 0.199
Sensitivity	0.337
Positive Predictive Value	0.769
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...	0.81	0.77	0.85	17	1088	3	0	3	0	5
3GX2_A	SAM links to Rfam database...	0.46	0.39	0.55	11	1429	10	2	7	1	17
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	25536	0	0	0	0	95
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...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.34	0.30	0.41	11	2251	18	1	15	2	26
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.71	1.00	17	849	0	0	0	0	7
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.42	0.34	0.53	10	1418	10	1	8	1	19
4ENB_A	crcB links to Rfam database...	0.44	0.20	1.00	3	469	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10

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