CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidHomfold‑LAST		Murlet(seed)
MCC	0.638	>	0.503
Average MCC ± 95% Confidence Intervals	0.644 ± 0.222	>	0.503 ± 0.153
Sensitivity	0.617	>	0.352
Positive Predictive Value	0.672	<	0.736
Total TP	156	>	89
Total TN	15012	<	15123
Total FP	92	>	34
Total FP CONTRA	26	>	2
Total FP INCONS	50	>	30
Total FP COMP	16	>	2
Total FN	97	<	164
P-value	8.61680779366e-09

Comparison of performance of CentroidHomfold-LAST 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 CentroidHomfold‑LAST and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST 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 CentroidHomfold‑LAST and Murlet(seed)).

Total Scores
MCC	0.638
Average MCC ± 95% Confidence Intervals	0.644 ± 0.222
Sensitivity	0.617
Positive Predictive Value	0.672
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	517	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
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...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.50	0.40	12	1172	18	6	12	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.37	0.46	0.32	13	1807	28	11	17	0	15

Total Scores
MCC	0.503
Average MCC ± 95% Confidence Intervals	0.503 ± 0.153
Sensitivity	0.352
Positive Predictive Value	0.736
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.57	0.39	0.88	7	349	2	0	1	1	11
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
3RKF_A	Purine links to Rfam database...	0.62	0.50	0.80	12	851	3	1	2	0	12
3SD1_A	THF links to Rfam database...	0.56	0.38	0.85	11	1520	2	0	2	0	18
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.27	0.75	9	1977	3	0	3	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.59	0.35	1.00	7	4509	0	0	0	0	13
4AOB_A	SAM links to Rfam database...	0.69	0.48	1.00	14	1423	1	0	0	1	15
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	3	1190	9	0	9	0	21
4FRN_A	AdoCbl-variant links to Rfam database...	0.66	0.50	0.88	14	1832	2	1	1	0	14

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