CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		CentroidHomfold‑LAST
MCC	0.595	>	0.572
Average MCC ± 95% Confidence Intervals	0.580 ± 0.165	<	0.584 ± 0.193
Sensitivity	0.539	<	0.578
Positive Predictive Value	0.667	>	0.576
Total TP	124	<	133
Total TN	20026	>	19981
Total FP	79	<	131
Total FP CONTRA	18	<	40
Total FP INCONS	44	<	58
Total FP COMP	17	<	33
Total FN	106	>	97
P-value	9.03109540436e-07

Comparison of performance of Murlet(20) and CentroidHomfold-LAST. 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 Murlet(20) and CentroidHomfold‑LAST).
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 Murlet(20) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and CentroidHomfold-LAST. 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 Murlet(20) and CentroidHomfold‑LAST).

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.580 ± 0.165
Sensitivity	0.539
Positive Predictive Value	0.667
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J3D_C	tRNA links to Rfam database...	0.84	0.84	0.84	16	949	3	3	0	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	5	2729	13	2	6	5	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.53	0.56	10	4743	13	2	6	5	9
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

Total Scores
MCC	0.572
Average MCC ± 95% Confidence Intervals	0.584 ± 0.193
Sensitivity	0.578
Positive Predictive Value	0.576
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.07	0.09	1	2731	16	4	6	6	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.27	9	4728	36	11	13	12	10
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
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

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