CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		CentroidAlifold(seed)
MCC	0.777	>	0.728
Average MCC ± 95% Confidence Intervals	0.770 ± 0.085	>	0.708 ± 0.063
Sensitivity	0.686	>	0.580
Positive Predictive Value	0.884	<	0.918
Total TP	478	>	404
Total TN	74688	<	74789
Total FP	141	>	89
Total FP CONTRA	21	>	17
Total FP INCONS	42	>	19
Total FP COMP	78	>	53
Total FN	219	<	293
P-value	5.23657817852e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	478
Total TN	74688
Total FP	141
Total FP CONTRA	21
Total FP INCONS	42
Total FP COMP	78
Total FN	219

Total Scores
MCC	0.777
Average MCC ± 95% Confidence Intervals	0.770 ± 0.085
Sensitivity	0.686
Positive Predictive Value	0.884
Nr of predictions	26

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2. Individual counts for RNAalifold(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...	0.51	0.50	0.56	9	341	8	0	7	1	9
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	3	0	0	3	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	0	0	0	0	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	0.78	0.95	18	884	1	1	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	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...	0.76	0.73	0.79	11	2364	20	0	3	17	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.77	0.83	0.71	10	4742	15	3	1	11	2
3LA5_A	Purine links to Rfam database...	0.87	0.76	1.00	19	935	0	0	0	0	6
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	404
Total TN	74789
Total FP	89
Total FP CONTRA	17
Total FP INCONS	19
Total FP COMP	53
Total FN	293

Total Scores
MCC	0.728
Average MCC ± 95% Confidence Intervals	0.708 ± 0.063
Sensitivity	0.580
Positive Predictive Value	0.918
Nr of predictions	26

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2. Individual counts for CentroidAlifold(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...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	0.47	0.22	1.00	2	1150	4	0	0	4	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.67	0.73	0.62	8	1822	22	0	5	17	3
2XQD_Y	tRNA links to Rfam database...	0.48	0.24	1.00	5	1124	1	0	0	1	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.83	0.74	0.93	26	2017	4	0	2	2	9
3A2K_C	tRNA links to Rfam database...	0.52	0.27	1.00	6	1102	0	0	0	0	16
3AMU_B	tRNA links to Rfam database...	0.51	0.26	1.00	5	1152	1	0	0	1	14
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...	0.58	0.43	0.77	41	25483	17	12	0	5	54
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.46	1.00	16	2624	0	0	0	0	19
3JYV_7	tRNA links to Rfam database...	0.50	0.25	1.00	5	1106	1	0	0	1	15
3JYX_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	8	2368	8	0	2	6	7
3JYX_4	5_8S_rRNA links to Rfam database...	0.91	0.83	1.00	10	4746	3	0	0	3	2
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...	0.79	0.65	0.96	24	2253	5	0	1	4	13
3O58_2	5S_rRNA links to Rfam database...	0.72	0.52	1.00	16	2738	0	0	0	0	15
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3PDR_A	ykoK links to Rfam database...	0.93	0.88	0.98	44	4795	3	0	1	2	6
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...	0.85	0.76	0.96	22	1510	1	0	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
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...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7

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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 RNAalifold(20) - scored higher in this pairwise comparison

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

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

Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

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

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