CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Murlet(seed)
MCC	0.491	>	0.403
Average MCC ± 95% Confidence Intervals	0.500 ± 0.145	>	0.406 ± 0.109
Sensitivity	0.397	>	0.213
Positive Predictive Value	0.613	<	0.767
Total TP	171	>	92
Total TN	74385	<	74544
Total FP	148	>	32
Total FP CONTRA	22	>	1
Total FP INCONS	86	>	27
Total FP COMP	40	>	4
Total FN	260	<	339
P-value	1.27752322258e-08

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

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.500 ± 0.145
Sensitivity	0.397
Positive Predictive Value	0.613
Nr of predictions	13

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	29	3	16	10	25
3W1K_J	tRNA-Sec links to Rfam database...	0.81	0.71	0.93	27	4157	2	1	1	0	11
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
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
4JF2_A	preQ1-II links to Rfam database...	0.50	0.39	0.67	12	2832	6	2	4	0	19

Total Scores
MCC	0.403
Average MCC ± 95% Confidence Intervals	0.406 ± 0.109
Sensitivity	0.213
Positive Predictive Value	0.767
Nr of predictions	13

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	1528	12	0	12	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.06	1.00	2	7501	2	0	0	2	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.19	1.00	7	12239	0	0	0	0	29
3W1K_J	tRNA-Sec links to Rfam database...	0.43	0.21	0.89	8	4177	1	0	1	0	30
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.23	0.75	9	4741	3	0	3	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.13	1.00	7	14189	0	0	0	0	45
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.15	0.09	0.25	3	3474	9	0	9	0	29
4FRN_A	AdoCbl-variant links to Rfam database...	0.58	0.39	0.88	14	5135	2	1	1	0	22
4JF2_A	preQ1-II links to Rfam database...	0.51	0.29	0.90	9	2840	2	0	1	1	22

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