CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold5		NanoFolder
MCC	0.428	>	0.358
Average MCC ± 95% Confidence Intervals	0.560 ± 0.154	>	0.529 ± 0.145
Sensitivity	0.372	>	0.368
Positive Predictive Value	0.500	>	0.358
Total TP	241	>	238
Total TN	89220	>	89037
Total FP	259	<	443
Total FP CONTRA	18	<	51
Total FP INCONS	223	<	376
Total FP COMP	18	>	16
Total FN	406	<	409
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Vsfold5 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 Vsfold5 and NanoFolder).
Comparison of performance of Vsfold5 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 Vsfold5 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 Vsfold5 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 Vsfold5 and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold5 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 Vsfold5 and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold5 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 Vsfold5 and NanoFolder).

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Performance of Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	241
Total TN	89220
Total FP	259
Total FP CONTRA	18
Total FP INCONS	223
Total FP COMP	18
Total FN	406

Total Scores
MCC	0.428
Average MCC ± 95% Confidence Intervals	0.560 ± 0.154
Sensitivity	0.372
Positive Predictive Value	0.500
Nr of predictions	22

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2. Individual counts for Vsfold5 [ 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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LDL_A	-	0.85	0.73	1.00	8	343	1	0	0	1	3
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2LKR_A	-	0.27	0.23	0.32	9	6077	19	2	17	0	30
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.45	0.71	24	7841	13	1	9	3	29
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.16	0.14	0.20	5	3545	20	1	19	0	32
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.76	0.70	0.82	28	4719	7	1	5	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.08	0.06	0.11	3	6994	24	0	24	0	46
3ZEX_E	-	0.07	0.06	0.08	5	21886	54	5	49	0	72
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ATO_G	-	0.56	0.60	0.55	6	517	5	1	4	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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	238
Total TN	89037
Total FP	443
Total FP CONTRA	51
Total FP INCONS	376
Total FP COMP	16
Total FN	409

Total Scores
MCC	0.358
Average MCC ± 95% Confidence Intervals	0.529 ± 0.145
Sensitivity	0.368
Positive Predictive Value	0.358
Nr of predictions	22

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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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3J20_1	tRNA links to Rfam database...	0.41	0.48	0.37	11	2896	19	5	14	0	12
3J2L_3	5S_rRNA links to Rfam database...	0.11	0.11	0.12	6	7824	46	3	42	1	47
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
3ZEX_E	-	0.03	0.04	0.03	3	21859	85	9	74	2	74
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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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 Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ 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 ]