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)		Contrafold
MCC	0.810	>	0.659
Average MCC ± 95% Confidence Intervals	0.802 ± 0.071	>	0.670 ± 0.117
Sensitivity	0.716	>	0.677
Positive Predictive Value	0.921	>	0.647
Total TP	499	>	472
Total TN	74687	>	74500
Total FP	122	<	363
Total FP CONTRA	21	<	89
Total FP INCONS	22	<	168
Total FP COMP	79	<	106
Total FN	198	<	225
P-value	5.19332990918e-08

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Performance plots

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

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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 Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	472
Total TN	74500
Total FP	363
Total FP CONTRA	89
Total FP INCONS	168
Total FP COMP	106
Total FN	225

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.670 ± 0.117
Sensitivity	0.677
Positive Predictive Value	0.647
Nr of predictions	26

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2. Individual counts for Contrafold [ 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	0.94	0.94	17	339	2	0	1	1	1
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.86	0.86	18	1108	4	0	3	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.12	4	2012	30	2	27	1	31
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3AMU_B	tRNA links to Rfam database...	0.75	0.79	0.71	15	1136	9	0	6	3	4
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
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...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.33	0.47	0.24	7	2349	24	16	6	2	8
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.58	0.27	7	4730	35	13	6	16	5
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...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_2	5S_rRNA links to Rfam database...	0.92	0.94	0.91	29	2722	10	0	3	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4A1C_3	5S_rRNA links to Rfam database...	0.81	0.81	0.81	30	2726	10	0	7	3	7
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

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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 Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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