CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		RSpredict(seed)
MCC	0.344	>	0.106
Average MCC ± 95% Confidence Intervals	0.361 ± 0.107	>	0.072 ± 0.079
Sensitivity	0.434	>	0.053
Positive Predictive Value	0.287	>	0.230
Total TP	188	>	23
Total TN	36872	<	37428
Total FP	544	>	83
Total FP CONTRA	161	>	14
Total FP INCONS	307	>	63
Total FP COMP	76	>	6
Total FN	245	<	410
P-value	3.05041766982e-08

Comparison of performance of NanoFolder and RSpredict(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 NanoFolder and RSpredict(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 NanoFolder and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for NanoFolder and RSpredict(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 NanoFolder and RSpredict(seed)).

Total Scores
MCC	0.344
Average MCC ± 95% Confidence Intervals	0.361 ± 0.107
Sensitivity	0.434
Positive Predictive Value	0.287
Nr of predictions	18

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...	0.54	0.61	0.50	11	506	11	1	10	0	7
3J16_L	tRNA links to Rfam database...	0.43	0.52	0.37	11	1129	19	8	11	0	10
3J20_1	tRNA links to Rfam database...	0.42	0.50	0.37	10	1085	20	5	12	3	10
3J2L_3	5S_rRNA links to Rfam database...	0.13	0.18	0.12	6	2969	46	14	31	1	28
3J3D_C	tRNA links to Rfam database...	0.76	0.95	0.62	18	939	11	9	2	0	1
3J3E_7	5S_rRNA links to Rfam database...	0.44	0.53	0.38	18	2693	31	10	20	1	16
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2707	47	11	24	12	15
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.25	0.18	9	2883	43	10	32	1	27
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.47	0.19	9	4714	57	21	17	19	10
3UZL_B	tRNA links to Rfam database...	0.41	0.56	0.31	9	1264	25	10	10	5	7
3W3S_B	tRNA-Sec links to Rfam database...	0.18	0.21	0.18	7	1949	34	2	31	1	26
3ZEX_D	5S_rRNA links to Rfam database...	0.30	0.37	0.27	13	2747	36	10	26	0	22
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	31	8	8	15	5
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4
4JF2_A	preQ1-II links to Rfam database...	0.55	0.67	0.47	16	1048	19	9	9	1	8

Total Scores
MCC	0.106
Average MCC ± 95% Confidence Intervals	0.072 ± 0.079
Sensitivity	0.053
Positive Predictive Value	0.230
Nr of predictions	18

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	515	13	0	13	0	18
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3J20_1	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	5	0	4	1	20
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3015	5	0	5	0	34
3J3D_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	964	4	1	3	0	19
3J3E_7	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2733	8	1	7	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2930	4	1	3	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	5	3	1	1	17
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.36	0.57	12	1968	10	1	8	1	21
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2794	2	0	2	0	35
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	4	0	2	2	8
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12
4JF2_A	preQ1-II links to Rfam database...	-0.01	0.00	0.00	0	1078	4	0	4	0	24

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