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)		UNAFold
MCC	0.659	>	0.589
Average MCC ± 95% Confidence Intervals	0.656 ± 0.071	>	0.601 ± 0.086
Sensitivity	0.510	<	0.513
Positive Predictive Value	0.854	>	0.681
Total TP	502	<	505
Total TN	198817	>	198663
Total FP	121	<	303
Total FP CONTRA	21	<	33
Total FP INCONS	65	<	204
Total FP COMP	35	<	66
Total FN	482	>	479
P-value	5.06544643719e-08

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Performance plots

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

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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	502
Total TN	198817
Total FP	121
Total FP CONTRA	21
Total FP INCONS	65
Total FP COMP	35
Total FN	482

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.656 ± 0.071
Sensitivity	0.510
Positive Predictive Value	0.854
Nr of predictions	25

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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
2KDQ_B	mir-TAR links to Rfam database...	0.60	0.36	1.00	4	402	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3G4S_9	5S_rRNA links to Rfam database...	0.69	0.49	0.97	28	7352	3	1	0	2	29
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.53	0.35	0.82	46	70820	15	4	6	5	86
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.59	0.86	32	6866	5	1	4	0	22
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.52	0.70	14	6308	17	0	6	11	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	15	0	10	5	23
3LA5_A	Purine links to Rfam database...	0.75	0.56	1.00	19	2466	0	0	0	0	15
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	3	1	0	2	24
3O58_2	5S_rRNA links to Rfam database...	0.79	0.76	0.83	29	7225	7	3	3	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.26	0.53	9	12386	8	2	6	0	26
3PDR_A	ykoK links to Rfam database...	0.76	0.61	0.96	44	12834	3	0	2	1	28
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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Performance of UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	505
Total TN	198663
Total FP	303
Total FP CONTRA	33
Total FP INCONS	204
Total FP COMP	66
Total FN	479

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.601 ± 0.086
Sensitivity	0.513
Positive Predictive Value	0.681
Nr of predictions	25

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2. Individual counts for UNAFold [ 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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.39	0.67	22	7348	11	1	10	0	35
3GX2_A	SAM links to Rfam database...	0.68	0.55	0.85	22	4345	5	0	4	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.51	0.45	0.58	60	70772	50	4	40	6	72
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3JYV_7	tRNA links to Rfam database...	0.22	0.19	0.29	6	2829	15	0	15	0	26
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	31	3	16	12	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.78	0.65	0.94	30	6989	5	0	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	4	7	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	33	1	21	11	23
3PDR_A	ykoK links to Rfam database...	0.77	0.64	0.94	46	12831	5	0	3	2	26
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.64	0.52	0.79	22	3888	6	1	5	0	20
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	5	26	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

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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 UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

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