CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	McQFold		Vsfold5
MCC	0.627	>	0.523
Average MCC ± 95% Confidence Intervals	0.657 ± 0.105	>	0.556 ± 0.102
Sensitivity	0.646	>	0.527
Positive Predictive Value	0.616	>	0.527
Total TP	615	>	502
Total TN	102161	<	102207
Total FP	459	<	530
Total FP CONTRA	150	<	158
Total FP INCONS	233	<	292
Total FP COMP	76	<	80
Total FN	337	<	450
P-value	3.56938820447e-08

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Performance plots

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

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Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	615
Total TN	102161
Total FP	459
Total FP CONTRA	150
Total FP INCONS	233
Total FP COMP	76
Total FN	337

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.657 ± 0.105
Sensitivity	0.646
Positive Predictive Value	0.616
Nr of predictions	39

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KRL_A	-	0.75	0.83	0.68	19	1996	15	7	2	6	4
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2M58_A	-	0.60	0.58	0.64	7	533	5	1	3	1	5
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	1	0	0	1	1
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.21	0.21	0.24	6	1447	19	2	17	0	22
3IYQ_A	tmRNA links to Rfam database...	0.22	0.31	0.15	16	22335	100	45	44	11	35
3IZ4_A	tmRNA links to Rfam database...	0.46	0.46	0.47	44	25442	56	14	36	6	51
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	36	8	16	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.42	0.23	8	4726	41	12	15	14	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.42	0.42	0.44	8	717	10	2	8	0	11
3NPB_A	SAM links to Rfam database...	0.90	0.81	1.00	30	2248	5	0	0	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
3PDR_A	ykoK links to Rfam database...	0.83	0.80	0.87	40	4794	9	2	4	3	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	1	4	0	5
3U4M_B	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	5	4	0	1	0
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	502
Total TN	102207
Total FP	530
Total FP CONTRA	158
Total FP INCONS	292
Total FP COMP	80
Total FN	450

Total Scores
MCC	0.523
Average MCC ± 95% Confidence Intervals	0.556 ± 0.102
Sensitivity	0.527
Positive Predictive Value	0.527
Nr of predictions	39

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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
2KFC_A	-	0.77	0.88	0.70	7	226	3	2	1	0	1
2KRL_A	-	0.71	0.78	0.64	18	1996	13	8	2	3	5
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3ADB_C	-	0.72	0.61	0.87	20	1796	3	0	3	0	13
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.61	0.57	0.67	16	1425	9	0	8	1	12
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.26	0.25	0.30	7	1449	16	2	14	0	21
3IYQ_A	tmRNA links to Rfam database...	0.30	0.37	0.24	19	22361	71	36	24	11	32
3IZ4_A	tmRNA links to Rfam database...	0.31	0.31	0.33	29	25448	65	14	45	6	66
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	31	10	12	9	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.27	9	4728	38	13	11	14	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3LA5_A	Purine links to Rfam database...	-0.02	0.00	0.00	0	938	16	0	16	0	25
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.62	0.54	0.71	20	2250	10	1	7	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.83	0.85	0.82	28	1955	7	2	4	1	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ATO_G	-	0.67	0.86	0.55	6	209	5	5	0	0	1
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.15	0.14	0.17	4	1825	19	3	16	0	24
4JF2_A	preQ1-II links to Rfam database...	0.96	1.00	0.92	24	1056	2	2	0	0	0
4JRC_A	-	0.28	0.29	0.31	5	606	11	2	9	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 McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]