CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		RDfolder
MCC	0.646	>	0.541
Average MCC ± 95% Confidence Intervals	0.630 ± 0.062	>	0.557 ± 0.164
Sensitivity	0.488	>	0.440
Positive Predictive Value	0.862	>	0.675
Total TP	231	>	208
Total TN	45318	>	45278
Total FP	45	<	109
Total FP CONTRA	7	<	14
Total FP INCONS	30	<	86
Total FP COMP	8	<	9
Total FN	242	<	265
P-value	2.41358941668e-08

Comparison of performance of Murlet(20) and RDfolder. 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 RDfolder).
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 RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and RDfolder. 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 RDfolder).

Total Scores
MCC	0.646
Average MCC ± 95% Confidence Intervals	0.630 ± 0.062
Sensitivity	0.488
Positive Predictive Value	0.862
Nr of predictions	17

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...	0.67	0.45	1.00	5	401	0	0	0	0	6
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2WRQ_Y	tRNA links to Rfam database...	0.41	0.41	0.41	7	2833	12	6	4	2	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.80	0.70	0.90	19	2829	2	0	2	0	8
3A2K_C	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	2	0	2	0	9
3AMU_B	tRNA links to Rfam database...	0.77	0.67	0.90	18	2983	3	0	2	1	9
3GX2_A	SAM links to Rfam database...	0.61	0.38	1.00	15	4356	1	0	0	1	25
3IVN_B	Purine links to Rfam database...	0.69	0.48	1.00	15	2331	0	0	0	0	16
3J20_0	tRNA links to Rfam database...	0.58	0.47	0.74	14	2831	5	0	5	0	16
3JYV_7	tRNA links to Rfam database...	0.67	0.53	0.85	17	2830	3	0	3	0	15
3LA5_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2469	0	0	0	0	18
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

Total Scores
MCC	0.541
Average MCC ± 95% Confidence Intervals	0.557 ± 0.164
Sensitivity	0.440
Positive Predictive Value	0.675
Nr of predictions	17

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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4538	22	5	17	0	20
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...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	1	8	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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