CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MXScarna(seed)
MCC	0.696	>	0.642
Average MCC ± 95% Confidence Intervals	0.660 ± 0.101	>	0.584 ± 0.119
Sensitivity	0.572	>	0.536
Positive Predictive Value	0.847	>	0.769
Total TP	687	>	644
Total TN	1197990	>	1197964
Total FP	151	<	229
Total FP CONTRA	15	<	26
Total FP INCONS	109	<	167
Total FP COMP	27	<	36
Total FN	515	<	558
P-value	3.18846395401e-08

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

Total Scores
MCC	0.696
Average MCC ± 95% Confidence Intervals	0.660 ± 0.101
Sensitivity	0.572
Positive Predictive Value	0.847
Nr of predictions	17

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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.73	0.61	0.87	387	1116318	63	8	52	3	246
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.33	0.50	12	5127	12	3	9	0	24

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.584 ± 0.119
Sensitivity	0.536
Positive Predictive Value	0.769
Nr of predictions	17

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...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.67	0.58	0.77	366	1116289	118	14	96	8	267
3J20_0	tRNA links to Rfam database...	0.79	0.63	1.00	19	2831	0	0	0	0	11
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	1	8	2	27
3UZL_B	tRNA links to Rfam database...	0.66	0.49	0.90	18	3550	2	1	1	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.69	0.60	0.80	24	4723	6	0	6	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	20	2	7	11	42
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.69	0.83	34	6980	7	1	6	0	15
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.31	0.56	10	3468	8	2	6	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.62	0.53	0.73	19	5125	7	2	5	0	17

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