CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Murlet(seed)
MCC	0.658	>	0.493
Average MCC ± 95% Confidence Intervals	0.633 ± 0.163	>	0.491 ± 0.109
Sensitivity	0.632	>	0.320
Positive Predictive Value	0.693	<	0.769
Total TP	223	>	113
Total TN	30202	<	30377
Total FP	136	>	39
Total FP CONTRA	35	>	3
Total FP INCONS	64	>	31
Total FP COMP	37	>	5
Total FN	130	<	240
P-value	1.86109605532e-08

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

Total Scores
MCC	0.658
Average MCC ± 95% Confidence Intervals	0.633 ± 0.163
Sensitivity	0.632
Positive Predictive Value	0.693
Nr of predictions	15

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...	0.41	0.33	0.55	6	517	5	1	4	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
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...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
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...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4JF2_A	preQ1-II links to Rfam database...	0.96	0.96	0.96	23	1058	1	1	0	0	1

Total Scores
MCC	0.493
Average MCC ± 95% Confidence Intervals	0.491 ± 0.109
Sensitivity	0.320
Positive Predictive Value	0.769
Nr of predictions	15

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.36	0.13	1.00	2	2740	2	0	0	2	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.61	0.37	1.00	7	4754	0	0	0	0	12
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
3W1K_J	tRNA-Sec links to Rfam database...	0.47	0.26	0.89	8	1669	1	0	1	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.27	0.75	9	1977	3	0	3	0	24
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	0	0	0	0	22
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
4JF2_A	preQ1-II links to Rfam database...	0.47	0.29	0.78	7	1073	4	1	1	2	17

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