CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		Vsfold4
MCC	0.637	>	0.537
Average MCC ± 95% Confidence Intervals	0.638 ± 0.105	>	0.566 ± 0.144
Sensitivity	0.538	>	0.531
Positive Predictive Value	0.760	>	0.551
Total TP	297	>	293
Total TN	62764	>	62623
Total FP	126	<	297
Total FP CONTRA	26	<	70
Total FP INCONS	68	<	169
Total FP COMP	32	<	58
Total FN	255	<	259
P-value	5.23657817852e-08

Comparison of performance of Murlet(20) and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and Vsfold4. 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 Vsfold4).

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.638 ± 0.105
Sensitivity	0.538
Positive Predictive Value	0.760
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.88	0.86	0.90	19	1087	2	0	2	0	3
3GX2_A	SAM links to Rfam database...	0.73	0.54	1.00	15	1434	1	0	0	1	13
3IVN_B	Purine links to Rfam database...	0.80	0.65	1.00	15	888	0	0	0	0	8
3IZ4_A	tmRNA links to Rfam database...	0.46	0.33	0.66	31	25489	22	3	13	6	64
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J3D_C	tRNA links to Rfam database...	0.84	0.84	0.84	16	949	3	3	0	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	5	2729	13	2	6	5	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.53	0.56	10	4743	13	2	6	5	9
3JYV_7	tRNA links to Rfam database...	0.84	0.80	0.89	16	1093	4	0	2	2	4
3LA5_A	Purine links to Rfam database...	0.80	0.64	1.00	16	938	0	0	0	0	9
3NPB_A	SAM links to Rfam database...	0.65	0.43	1.00	16	2262	2	0	0	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	3	1	2	0	12
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

Total Scores
MCC	0.537
Average MCC ± 95% Confidence Intervals	0.566 ± 0.144
Sensitivity	0.531
Positive Predictive Value	0.551
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	0	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
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...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
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...	0.23	0.24	0.24	7	1504	22	5	17	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
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...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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