CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Pknots		Murlet(seed)
MCC	0.695	>	0.571
Average MCC ± 95% Confidence Intervals	0.728 ± 0.157	>	0.568 ± 0.104
Sensitivity	0.712	>	0.386
Positive Predictive Value	0.686	<	0.855
Total TP	260	>	141
Total TN	26157	<	26371
Total FP	153	>	29
Total FP CONTRA	42	>	4
Total FP INCONS	77	>	20
Total FP COMP	34	>	5
Total FN	105	<	224
P-value	2.57237423209e-08

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

Total Scores
MCC	0.695
Average MCC ± 95% Confidence Intervals	0.728 ± 0.157
Sensitivity	0.712
Positive Predictive Value	0.686
Nr of predictions	14

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...	0.83	0.83	0.83	15	510	3	2	1	0	3
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.568 ± 0.104
Sensitivity	0.386
Positive Predictive Value	0.855
Nr of predictions	14

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	516	12	0	12	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.63	0.40	1.00	12	1488	0	0	0	0	18
3GX2_A	SAM links to Rfam database...	0.70	0.50	1.00	14	1435	1	0	0	1	14
3IVN_B	Purine links to Rfam database...	0.62	0.52	0.75	12	887	4	2	2	0	11
3LA5_A	Purine links to Rfam database...	0.67	0.56	0.82	14	937	3	1	2	0	11
3NPB_A	SAM links to Rfam database...	0.59	0.35	1.00	13	2265	2	0	0	2	24
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.27	1.00	6	4758	1	0	0	1	16
3PDR_A	ykoK links to Rfam database...	0.53	0.28	1.00	14	4826	0	0	0	0	36
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
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

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