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		Vsfold5
MCC	0.784	>	0.507
Average MCC ± 95% Confidence Intervals	0.782 ± 0.101	>	0.603 ± 0.120
Sensitivity	0.759	>	0.514
Positive Predictive Value	0.816	>	0.515
Total TP	542	>	367
Total TN	49324	>	49275
Total FP	183	<	396
Total FP CONTRA	39	<	94
Total FP INCONS	83	<	252
Total FP COMP	61	>	50
Total FN	172	<	347
P-value	3.56938820447e-08

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Performance plots

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

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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	542
Total TN	49324
Total FP	183
Total FP CONTRA	39
Total FP INCONS	83
Total FP COMP	61
Total FN	172

Total Scores
MCC	0.784
Average MCC ± 95% Confidence Intervals	0.782 ± 0.101
Sensitivity	0.759
Positive Predictive Value	0.816
Nr of predictions	39

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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...	0.58	0.56	0.63	10	512	6	0	6	0	8
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	0.92	0.86	1.00	6	124	3	0	0	3	1
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.70	0.66	0.76	19	2415	12	0	6	6	10
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
3J0L_2	-	0.80	0.77	0.83	20	2226	11	0	4	7	6
3J0L_1	-	0.75	0.69	0.82	9	473	5	0	2	3	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_h	-	0.95	0.91	1.00	29	2111	2	0	0	2	3
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	3	0	2	1	2
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2C_O	-	1.00	1.00	1.00	41	3946	4	0	0	4	0
3J2L_3	5S_rRNA links to Rfam database...	0.95	0.91	1.00	31	2989	4	0	0	4	3
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
3ZEX_D	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2766	4	0	0	4	5
3ZEX_E	-	0.12	0.15	0.10	5	8255	44	20	24	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17

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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	367
Total TN	49275
Total FP	396
Total FP CONTRA	94
Total FP INCONS	252
Total FP COMP	50
Total FN	347

Total Scores
MCC	0.507
Average MCC ± 95% Confidence Intervals	0.603 ± 0.120
Sensitivity	0.514
Positive Predictive Value	0.515
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
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
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.31	0.31	0.32	9	2412	19	5	14	0	20
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J0L_2	-	0.42	0.42	0.44	11	2225	21	1	13	7	15
3J0L_1	-	0.25	0.23	0.30	3	474	8	3	4	1	10
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_h	-	0.20	0.19	0.24	6	2115	19	3	16	0	26
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J2C_O	-	0.33	0.32	0.36	13	3951	26	3	20	3	28
3J2L_3	5S_rRNA links to Rfam database...	0.70	0.71	0.71	24	2986	13	3	7	3	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.24	0.31	0.20	5	1268	20	9	11	0	11
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.83	0.85	0.82	28	1955	7	2	4	1	5
3ZEX_D	5S_rRNA links to Rfam database...	0.09	0.09	0.12	3	2771	24	5	17	2	32
3ZEX_E	-	0.11	0.15	0.09	5	8247	54	21	31	2	29
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
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

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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 Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

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