CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	HotKnots		Murlet(seed)
MCC	0.642	>	0.534
Average MCC ± 95% Confidence Intervals	0.659 ± 0.139	>	0.529 ± 0.077
Sensitivity	0.673	>	0.349
Positive Predictive Value	0.621	<	0.828
Total TP	382	>	198
Total TN	46597	<	46973
Total FP	288	>	50
Total FP CONTRA	84	>	6
Total FP INCONS	149	>	35
Total FP COMP	55	>	9
Total FN	186	<	370
P-value	5.1503931209e-08

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

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.659 ± 0.139
Sensitivity	0.673
Positive Predictive Value	0.621
Nr of predictions	22

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...	0.64	0.61	0.69	11	512	5	0	5	0	7
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...	0.81	0.79	0.85	22	1423	5	2	2	1	6
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...	0.15	0.20	0.12	3	2717	33	7	15	11	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	43	11	12	20	11
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.36	0.19	8	4722	35	16	18	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.80	0.82	40	4791	11	3	6	2	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
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...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_C	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	5328	46	11	35	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	4	4	0	0	0

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.529 ± 0.077
Sensitivity	0.349
Positive Predictive Value	0.828
Nr of predictions	22

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
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
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
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.