CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		NanoFolder
MCC	0.556	>	0.272
Average MCC ± 95% Confidence Intervals	0.542 ± 0.122	>	0.326 ± 0.081
Sensitivity	0.451	>	0.284
Positive Predictive Value	0.691	>	0.269
Total TP	446	>	281
Total TN	155633	>	155234
Total FP	243	<	805
Total FP CONTRA	23	<	93
Total FP INCONS	176	<	670
Total FP COMP	44	>	42
Total FN	543	<	708
P-value	5.06544643719e-08

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Performance plots

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	446
Total TN	155633
Total FP	243
Total FP CONTRA	23
Total FP INCONS	176
Total FP COMP	44
Total FN	543

Total Scores
MCC	0.556
Average MCC ± 95% Confidence Intervals	0.542 ± 0.122
Sensitivity	0.451
Positive Predictive Value	0.691
Nr of predictions	26

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2. Individual counts for ContextFold [ 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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
2M58_A	-	-0.01	0.00	0.00	0	1639	14	0	14	0	17
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3J3D_C	tRNA links to Rfam database...	0.73	0.61	0.89	17	2756	2	0	2	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.72	0.56	0.94	30	7108	2	0	2	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	29	3	16	10	25
3J3F_7	5S_rRNA links to Rfam database...	0.81	0.68	0.97	34	7225	1	0	1	0	16
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.58	1.00	33	6988	0	0	0	0	24
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
3ZEX_G	-	0.26	0.20	0.33	15	16426	34	2	28	4	59
3ZEX_E	-	0.08	0.06	0.10	5	21896	44	5	39	0	72
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.22	5	2980	20	0	18	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ATO_G	-	-0.01	0.00	0.00	0	526	2	0	2	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4JF2_A	preQ1-II links to Rfam database...	0.50	0.39	0.67	12	2832	6	2	4	0	19
4JRC_A	-	0.78	0.61	1.00	14	1526	0	0	0	0	9

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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	281
Total TN	155234
Total FP	805
Total FP CONTRA	93
Total FP INCONS	670
Total FP COMP	42
Total FN	708

Total Scores
MCC	0.272
Average MCC ± 95% Confidence Intervals	0.326 ± 0.081
Sensitivity	0.284
Positive Predictive Value	0.269
Nr of predictions	26

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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
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2M58_A	-	0.43	0.47	0.40	8	1633	12	4	8	0	9
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
3J3D_C	tRNA links to Rfam database...	0.70	0.71	0.69	20	2746	9	2	7	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3J3E_7	5S_rRNA links to Rfam database...	0.35	0.33	0.37	18	7091	31	1	30	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.22	12	12192	54	9	33	12	24
3J3F_7	5S_rRNA links to Rfam database...	0.17	0.18	0.17	9	7208	43	3	40	0	41
3J3V_B	5S_rRNA links to Rfam database...	0.24	0.23	0.27	13	6973	35	1	34	0	44
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
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_G	-	0.05	0.05	0.05	4	16393	76	5	69	2	70
3ZEX_E	-	0.03	0.04	0.03	3	21859	85	9	74	2	74
3ZND_W	tRNA links to Rfam database...	0.18	0.22	0.17	5	2973	29	6	19	4	18
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
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
4JF2_A	preQ1-II links to Rfam database...	0.51	0.55	0.49	17	2815	18	5	13	0	14
4JRC_A	-	0.48	0.48	0.50	11	1518	11	0	11	0	12

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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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

2. Individual counts for ContextFold [ 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 ]