CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Vsfold4		NanoFolder
MCC	0.571	>	0.394
Average MCC ± 95% Confidence Intervals	0.676 ± 0.131	>	0.582 ± 0.147
Sensitivity	0.570	>	0.485
Positive Predictive Value	0.583	>	0.334
Total TP	288	>	245
Total TN	40735	>	40496
Total FP	241	<	536
Total FP CONTRA	55	<	162
Total FP INCONS	151	<	326
Total FP COMP	35	<	48
Total FN	217	<	260
P-value	5.23657817852e-08

^top

Performance plots

Comparison of performance of Vsfold4 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 Vsfold4 and NanoFolder).
Comparison of performance of Vsfold4 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 Vsfold4 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 Vsfold4 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 Vsfold4 and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold4 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 Vsfold4 and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold4 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 Vsfold4 and NanoFolder).

^top

Performance of Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	288
Total TN	40735
Total FP	241
Total FP CONTRA	55
Total FP INCONS	151
Total FP COMP	35
Total FN	217

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.676 ± 0.131
Sensitivity	0.570
Positive Predictive Value	0.583
Nr of predictions	25

^top

2. Individual counts for Vsfold4 [ 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	515	13	0	13	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
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	-	0.35	0.38	0.34	11	2408	21	7	14	0	18
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...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	12	3	6	3	10
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...	0.66	0.69	0.65	11	1276	10	3	3	4	5
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
3ZEX_G	-	0.31	0.29	0.34	13	6469	31	5	20	6	32
3ZEX_D	5S_rRNA links to Rfam database...	0.66	0.63	0.71	22	2765	10	4	5	1	13
3ZEX_E	-	0.12	0.15	0.11	5	8259	40	13	27	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

^top

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

^top

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

^top

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 Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ 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 ]