CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		MCFold
MCC	0.562	>	0.449
Average MCC ± 95% Confidence Intervals	0.537 ± 0.197	>	0.453 ± 0.199
Sensitivity	0.486	<	0.514
Positive Predictive Value	0.658	>	0.401
Total TP	123	<	130
Total TN	28382	>	28245
Total FP	98	<	250
Total FP CONTRA	21	<	67
Total FP INCONS	43	<	127
Total FP COMP	34	<	56
Total FN	130	>	123
P-value	1.70887622364e-08

Comparison of performance of RNASampler(seed) and MCFold. 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 RNASampler(seed) and MCFold).
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 RNASampler(seed) and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and MCFold. 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 RNASampler(seed) and MCFold).

Total Scores
MCC	0.562
Average MCC ± 95% Confidence Intervals	0.537 ± 0.197
Sensitivity	0.486
Positive Predictive Value	0.658
Nr of predictions	11

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...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.60	1.00	18	1482	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.18	0.20	0.18	3	2725	22	5	9	8	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.47	0.47	0.47	9	4742	18	5	5	8	10
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12
4JF2_A	preQ1-II links to Rfam database...	0.64	0.42	1.00	10	1072	0	0	0	0	14

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.453 ± 0.199
Sensitivity	0.514
Positive Predictive Value	0.401
Nr of predictions	11

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...	0.44	0.44	0.47	8	511	10	0	9	1	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2716	36	11	12	13	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.21	0.10	4	4720	51	17	20	14	15
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.27	10	5337	28	6	21	1	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4JF2_A	preQ1-II links to Rfam database...	0.74	0.75	0.75	18	1058	7	1	5	1	6

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