CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		MCFold
MCC	0.810	>	0.520
Average MCC ± 95% Confidence Intervals	0.806 ± 0.089	>	0.519 ± 0.113
Sensitivity	0.734	>	0.579
Positive Predictive Value	0.897	>	0.479
Total TP	401	>	316
Total TN	45705	>	45492
Total FP	128	<	439
Total FP CONTRA	19	<	110
Total FP INCONS	27	<	234
Total FP COMP	82	<	95
Total FN	145	<	230
P-value	5.19332990918e-08

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Performance plots

Comparison of performance of RNASampler(20) and MCFold. 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 RNASampler(20) and MCFold).
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 RNASampler(20) and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and MCFold. 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 RNASampler(20) and MCFold).

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

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

Total Base Pair Counts
Total TP	401
Total TN	45705
Total FP	128
Total FP CONTRA	19
Total FP INCONS	27
Total FP COMP	82
Total FN	145

Total Scores
MCC	0.810
Average MCC ± 95% Confidence Intervals	0.806 ± 0.089
Sensitivity	0.734
Positive Predictive Value	0.897
Nr of predictions	24

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
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...	0.60	0.36	1.00	4	1831	2	0	0	2	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...	0.34	0.11	1.00	4	2041	0	0	0	0	31
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...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2610	2	0	0	2	5
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...	0.70	0.60	0.82	9	2367	14	0	2	12	6
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	26	10	2	14	2
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	5	0	0	5	4
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
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...	0.81	0.69	0.95	20	1512	1	0	1	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	316
Total TN	45492
Total FP	439
Total FP CONTRA	110
Total FP INCONS	234
Total FP COMP	95
Total FN	230

Total Scores
MCC	0.520
Average MCC ± 95% Confidence Intervals	0.519 ± 0.113
Sensitivity	0.579
Positive Predictive Value	0.479
Nr of predictions	24

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	1	0	0	1	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.38	0.56	0.26	5	1133	21	8	6	7	4
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.27	0.16	3	1816	30	4	12	14	8
2XQD_Y	tRNA links to Rfam database...	0.39	0.43	0.38	9	1105	18	2	13	3	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
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...	0.50	0.58	0.44	11	1132	15	4	10	1	8
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.94	0.89	33	2603	10	0	4	6	2
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3JYX_3	5S_rRNA links to Rfam database...	0.46	0.67	0.32	10	2347	28	15	6	7	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.58	0.23	7	4725	37	19	5	13	5
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3O58_2	5S_rRNA links to Rfam database...	0.25	0.29	0.23	9	2715	31	6	24	1	22
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

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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 RNASampler(20) - scored higher in this pairwise comparison

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

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

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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