CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		NanoFolder
MCC	0.601	>	0.429
Average MCC ± 95% Confidence Intervals	0.702 ± 0.132	>	0.605 ± 0.145
Sensitivity	0.624	>	0.516
Positive Predictive Value	0.589	>	0.373
Total TP	294	>	243
Total TN	32426	>	32274
Total FP	252	<	450
Total FP CONTRA	55	<	131
Total FP INCONS	150	<	277
Total FP COMP	47	>	42
Total FN	177	<	228
P-value	5.1503931209e-08

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Performance plots

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

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	294
Total TN	32426
Total FP	252
Total FP CONTRA	55
Total FP INCONS	150
Total FP COMP	47
Total FN	177

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.702 ± 0.132
Sensitivity	0.624
Positive Predictive Value	0.589
Nr of predictions	24

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2. Individual counts for Pknots [ 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...	0.83	0.83	0.83	15	510	3	2	1	0	3
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	-	0.48	0.55	0.43	16	2403	23	9	12	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.38	0.27	0.60	3	202	3	0	2	1	8
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.79	0.79	27	2986	12	1	6	5	7
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.78	0.76	0.81	25	1958	7	1	5	1	8
3ZEX_G	-	0.45	0.49	0.42	22	6455	39	9	21	9	23
3ZEX_D	5S_rRNA links to Rfam database...	0.31	0.34	0.30	12	2756	28	5	23	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
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	243
Total TN	32274
Total FP	450
Total FP CONTRA	131
Total FP INCONS	277
Total FP COMP	42
Total FN	228

Total Scores
MCC	0.429
Average MCC ± 95% Confidence Intervals	0.605 ± 0.145
Sensitivity	0.516
Positive Predictive Value	0.373
Nr of predictions	24

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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
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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ 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 ]