CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(20)		MCFold
MCC	0.680	>	0.425
Average MCC ± 95% Confidence Intervals	0.689 ± 0.085	>	0.427 ± 0.099
Sensitivity	0.546	>	0.448
Positive Predictive Value	0.850	>	0.410
Total TP	386	>	317
Total TN	109302	>	108982
Total FP	114	<	501
Total FP CONTRA	13	<	72
Total FP INCONS	55	<	385
Total FP COMP	46	>	44
Total FN	321	<	390
P-value	5.1503931209e-08

Comparison of performance of RNASampler(20) and MCFold. 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 RNASampler(20) and MCFold).
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 RNASampler(20) and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and MCFold. 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 RNASampler(20) and MCFold).

Total Scores
MCC	0.680
Average MCC ± 95% Confidence Intervals	0.689 ± 0.085
Sensitivity	0.546
Positive Predictive Value	0.850
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZF_C	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	6871	1	0	1	0	23
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	26	4	15	7	23
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.44	0.75	12	6312	11	0	4	7	15
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	18	2	8	8	23
3O58_2	5S_rRNA links to Rfam database...	0.79	0.71	0.87	27	7229	5	2	2	1	11
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	5	0	3	2	34
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.67	0.48	0.95	20	3895	1	0	1	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Total Scores
MCC	0.425
Average MCC ± 95% Confidence Intervals	0.427 ± 0.099
Sensitivity	0.448
Positive Predictive Value	0.410
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	1	0	0	1	1
2WRQ_Y	tRNA links to Rfam database...	0.27	0.35	0.22	6	2823	25	8	13	4	11
2XQD_Y	tRNA links to Rfam database...	0.34	0.37	0.32	10	2819	22	1	20	1	17
3A2K_C	tRNA links to Rfam database...	0.44	0.46	0.42	13	2895	18	2	16	0	15
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3GX2_A	SAM links to Rfam database...	0.47	0.48	0.48	19	4331	22	0	21	1	21
3IVN_B	Purine links to Rfam database...	0.39	0.39	0.40	12	2316	18	0	18	0	19
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.69	0.74	37	6853	14	0	13	1	17
3JYV_7	tRNA links to Rfam database...	0.21	0.22	0.21	7	2817	26	0	26	0	25
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.24	0.17	8	12199	43	16	23	4	25
3JYX_3	5S_rRNA links to Rfam database...	0.41	0.52	0.33	14	6285	34	12	17	5	13
3LA5_A	Purine links to Rfam database...	0.32	0.32	0.34	11	2453	21	1	20	0	23
3O58_3	5_8S_rRNA links to Rfam database...	0.22	0.26	0.19	9	12355	45	9	30	6	26
3O58_2	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7208	44	5	38	1	29
3PDR_A	ykoK links to Rfam database...	0.66	0.61	0.72	44	12819	19	0	17	2	28
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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