CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	UNAFold		Vsfold4
MCC	0.596	>	0.553
Average MCC ± 95% Confidence Intervals	0.588 ± 0.096	>	0.572 ± 0.102
Sensitivity	0.621	>	0.549
Positive Predictive Value	0.580	>	0.565
Total TP	574	>	507
Total TN	100321	<	100413
Total FP	521	>	468
Total FP CONTRA	147	>	128
Total FP INCONS	269	>	263
Total FP COMP	105	>	77
Total FN	350	<	417
P-value	3.56938820447e-08

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Performance plots

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

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	574
Total TN	100321
Total FP	521
Total FP CONTRA	147
Total FP INCONS	269
Total FP COMP	105
Total FN	350

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.588 ± 0.096
Sensitivity	0.621
Positive Predictive Value	0.580
Nr of predictions	38

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	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...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
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...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	96	46	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.58	0.60	0.57	57	25436	53	12	31	10	38
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.33	0.37	0.32	7	946	15	3	12	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.13	3	2718	32	6	15	11	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.42	0.25	8	4729	44	12	12	20	11
3JYV_7	tRNA links to Rfam database...	0.24	0.25	0.25	5	1091	16	7	8	1	15
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	34	5	15	14	11
3PDR_A	ykoK links to Rfam database...	0.93	0.92	0.94	46	4791	5	1	2	2	4
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.61	0.61	0.63	20	1957	13	4	8	1	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	11	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	507
Total TN	100413
Total FP	468
Total FP CONTRA	128
Total FP INCONS	263
Total FP COMP	77
Total FN	417

Total Scores
MCC	0.553
Average MCC ± 95% Confidence Intervals	0.572 ± 0.102
Sensitivity	0.549
Positive Predictive Value	0.565
Nr of predictions	38

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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
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KRL_A	-	0.84	0.83	0.86	19	2002	9	2	1	6	4
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2M58_A	-	-0.02	0.00	0.00	0	538	6	0	6	0	12
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	-	0.95	0.91	1.00	30	1789	0	0	0	0	3
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	0	9	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...	0.28	0.25	0.35	7	1452	13	2	11	0	21
3IYQ_A	tmRNA links to Rfam database...	0.27	0.35	0.21	18	22353	80	40	29	11	33
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
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...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
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...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.23	0.24	0.24	7	1504	22	5	17	0	22
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
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
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4JF2_A	preQ1-II links to Rfam database...	0.74	0.67	0.84	16	1063	3	0	3	0	8
4JRC_A	-	0.34	0.29	0.42	5	610	7	0	7	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 UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

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

Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]