CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(20)		Vsfold4
MCC	0.810	>	0.530
Average MCC ± 95% Confidence Intervals	0.802 ± 0.071	>	0.572 ± 0.136
Sensitivity	0.716	>	0.524
Positive Predictive Value	0.921	>	0.545
Total TP	499	>	365
Total TN	74687	>	74559
Total FP	122	<	389
Total FP CONTRA	21	<	77
Total FP INCONS	22	<	228
Total FP COMP	79	<	84
Total FN	198	<	332
P-value	5.19332990918e-08

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Performance plots

Comparison of performance of CentroidAlifold(20) 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 CentroidAlifold(20) 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 CentroidAlifold(20) and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) 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 CentroidAlifold(20) and Vsfold4).

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Performance of CentroidAlifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(20)

Total Base Pair Counts
Total TP	499
Total TN	74687
Total FP	122
Total FP CONTRA	21
Total FP INCONS	22
Total FP COMP	79
Total FN	198

Total Scores
MCC	0.810
Average MCC ± 95% Confidence Intervals	0.802 ± 0.071
Sensitivity	0.716
Positive Predictive Value	0.921
Nr of predictions	26

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2. Individual counts for CentroidAlifold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.59	0.56	0.67	10	342	6	0	5	1	8
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	7	0	0	7	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	4	0	0	4	28
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.67	0.52	0.88	49	25480	9	7	0	2	46
3IZF_C	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2607	6	0	2	4	4
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_3	5S_rRNA links to Rfam database...	0.80	0.80	0.80	12	2363	23	0	3	20	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.67	0.75	0.60	9	4741	9	5	1	3	3
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.65	0.92	24	2252	6	1	1	4	13
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	9	0	2	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.64	0.45	0.91	10	4753	2	1	0	1	12
3PDR_A	ykoK links to Rfam database...	0.92	0.90	0.94	45	4792	5	1	2	2	5
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	4	0	2	2	3
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
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...	0.68	0.47	1.00	7	489	0	0	0	0	8

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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	365
Total TN	74559
Total FP	389
Total FP CONTRA	77
Total FP INCONS	228
Total FP COMP	84
Total FN	332

Total Scores
MCC	0.530
Average MCC ± 95% Confidence Intervals	0.572 ± 0.136
Sensitivity	0.524
Positive Predictive Value	0.545
Nr of predictions	26

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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
2L94_A	HIV_FE links to Rfam database...	0.94	0.89	1.00	16	341	1	0	0	1	2
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	13	0	0	13	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1808	27	13	14	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2016	29	1	28	0	35
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3AMU_B	tRNA links to Rfam database...	0.73	0.74	0.74	14	1138	8	0	5	3	5
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
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	6	0	4	2	6
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.67	0.63	10	2362	16	5	1	10	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	3	4736	33	9	8	16	9
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_2	5S_rRNA links to Rfam database...	0.53	0.52	0.55	16	2725	16	3	10	3	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
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
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
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

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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 CentroidAlifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(20)

2. Individual counts for CentroidAlifold(20) [ 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 ]