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)		MXScarna(seed)
MCC	0.810	>	0.780
Average MCC ± 95% Confidence Intervals	0.802 ± 0.071	>	0.768 ± 0.063
Sensitivity	0.716	<	0.739
Positive Predictive Value	0.921	>	0.827
Total TP	499	<	515
Total TN	74687	>	74606
Total FP	122	<	244
Total FP CONTRA	21	<	45
Total FP INCONS	22	<	63
Total FP COMP	79	<	136
Total FN	198	>	182
P-value	5.1503931209e-08

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Performance plots

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

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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 MXScarna(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for MXScarna(seed)

Total Base Pair Counts
Total TP	515
Total TN	74606
Total FP	244
Total FP CONTRA	45
Total FP INCONS	63
Total FP COMP	136
Total FN	182

Total Scores
MCC	0.780
Average MCC ± 95% Confidence Intervals	0.768 ± 0.063
Sensitivity	0.739
Positive Predictive Value	0.827
Nr of predictions	26

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2. Individual counts for MXScarna(seed) [ 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...	0.55	0.56	0.59	10	340	8	0	7	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...	0.78	0.82	0.75	9	1823	20	0	3	17	2
2XQD_Y	tRNA links to Rfam database...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.74	0.69	0.80	24	2015	7	0	6	1	11
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...	0.97	0.95	1.00	18	1139	2	0	0	2	1
3GX2_A	SAM links to Rfam database...	0.83	0.82	0.85	23	1422	7	2	2	3	5
3IVN_B	Purine links to Rfam database...	0.69	0.57	0.87	13	888	2	2	0	0	10
3IZ4_A	tmRNA links to Rfam database...	0.73	0.64	0.82	61	25462	22	12	1	9	34
3IZF_C	5S_rRNA links to Rfam database...	0.84	0.83	0.85	29	2606	11	0	5	6	6
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	21	6	1	14	2
3LA5_A	Purine links to Rfam database...	0.82	0.72	0.95	18	935	1	1	0	0	7
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	26	2247	10	2	3	5	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	11	0	2	9	2
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	20	5	3	12	11
3PDR_A	ykoK links to Rfam database...	0.87	0.88	0.86	44	4789	10	4	3	3	6
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...	0.74	0.76	0.73	22	1503	9	4	4	1	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4A1C_3	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	2726	6	0	3	3	3
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

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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 MXScarna(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for MXScarna(seed)

2. Individual counts for MXScarna(seed) [ download as .csv ]