CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAsubopt		NanoFolder
MCC	0.656	>	0.394
Average MCC ± 95% Confidence Intervals	0.712 ± 0.138	>	0.582 ± 0.147
Sensitivity	0.683	>	0.485
Positive Predictive Value	0.638	>	0.334
Total TP	345	>	245
Total TN	40688	>	40496
Total FP	261	<	536
Total FP CONTRA	62	<	162
Total FP INCONS	134	<	326
Total FP COMP	65	>	48
Total FN	160	<	260
P-value	5.23657817852e-08

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Performance plots

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

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Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	345
Total TN	40688
Total FP	261
Total FP CONTRA	62
Total FP INCONS	134
Total FP COMP	65
Total FN	160

Total Scores
MCC	0.656
Average MCC ± 95% Confidence Intervals	0.712 ± 0.138
Sensitivity	0.683
Positive Predictive Value	0.638
Nr of predictions	25

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2. Individual counts for RNAsubopt [ download as .csv ]

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	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.85	0.86	0.83	25	2410	14	0	5	9	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J16_L	tRNA links to Rfam database...	0.49	0.52	0.48	11	1136	12	3	9	0	10
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	3	0	0	3	0
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	13	1	7	5	6
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.94	0.97	31	1957	2	0	1	1	2
3ZEX_G	-	0.59	0.64	0.55	29	6454	34	12	12	10	16
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
3ZEX_E	-	0.00	0.00	0.00	0	8255	54	17	32	5	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	245
Total TN	40496
Total FP	536
Total FP CONTRA	162
Total FP INCONS	326
Total FP COMP	48
Total FN	260

Total Scores
MCC	0.394
Average MCC ± 95% Confidence Intervals	0.582 ± 0.147
Sensitivity	0.485
Positive Predictive Value	0.334
Nr of predictions	25

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2. Individual counts for NanoFolder [ download as .csv ]

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
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.26	0.34	0.21	10	2392	41	15	23	3	19
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
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
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.77	0.91	0.67	20	1246	12	6	4	2	2
3UZL_B	tRNA links to Rfam database...	0.41	0.56	0.31	9	1264	25	10	10	5	7
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.18	0.21	0.18	7	1949	34	2	31	1	26
3ZEX_G	-	0.04	0.07	0.04	3	6431	77	18	55	4	42
3ZEX_D	5S_rRNA links to Rfam database...	0.30	0.37	0.27	13	2747	36	10	26	0	22
3ZEX_E	-	0.03	0.06	0.02	2	8222	86	31	49	6	32
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4
4HXH_A	-	0.80	1.00	0.67	6	86	3	3	0	0	0

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

Table of contents:

Overview

Performance plots

Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

2. Individual counts for RNAsubopt [ download as .csv ]

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

2. Individual counts for NanoFolder [ download as .csv ]