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(seed)		Sfold
MCC	0.728	>	0.614
Average MCC ± 95% Confidence Intervals	0.632 ± 0.097	<	0.656 ± 0.103
Sensitivity	0.607	<	0.610
Positive Predictive Value	0.872	>	0.619
Total TP	684	<	687
Total TN	516772	>	516447
Total FP	175	<	567
Total FP CONTRA	38	<	129
Total FP INCONS	62	<	293
Total FP COMP	75	<	145
Total FN	442	>	439
P-value	5.10776592382e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	684
Total TN	516772
Total FP	175
Total FP CONTRA	38
Total FP INCONS	62
Total FP COMP	75
Total FN	442

Total Scores
MCC	0.728
Average MCC ± 95% Confidence Intervals	0.632 ± 0.097
Sensitivity	0.607
Positive Predictive Value	0.872
Nr of predictions	25

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.79	0.63	1.00	19	1481	0	0	0	0	11
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...	0.71	0.65	0.79	15	884	4	2	2	0	8
3IYQ_A	tmRNA links to Rfam database...	0.36	0.27	0.48	14	22411	19	13	2	4	37
3IZ4_A	tmRNA links to Rfam database...	0.46	0.26	0.81	25	25505	8	6	0	2	70
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.85	0.83	0.87	343	421974	104	11	40	53	69
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.61	0.37	1.00	7	4754	2	0	0	2	12
3LA5_A	Purine links to Rfam database...	0.73	0.64	0.84	16	935	3	1	2	0	9
3NPB_A	SAM links to Rfam database...	0.77	0.59	1.00	22	2256	3	0	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.66	1.00	33	4807	1	0	0	1	17
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.61	1.00	19	1659	0	0	0	0	12
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.52	1.00	17	1972	2	0	0	2	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	2	0	0	2	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
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...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.78	0.68	0.90	19	1827	2	1	1	0	9
4JF2_A	preQ1-II links to Rfam database...	0.61	0.42	0.91	10	1071	1	1	0	0	14

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Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	687
Total TN	516447
Total FP	567
Total FP CONTRA	129
Total FP INCONS	293
Total FP COMP	145
Total FN	439

Total Scores
MCC	0.614
Average MCC ± 95% Confidence Intervals	0.656 ± 0.103
Sensitivity	0.610
Positive Predictive Value	0.619
Nr of predictions	25

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	0	5	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.86	0.79	0.96	22	1426	2	1	0	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.25	0.33	0.19	17	22350	86	39	34	13	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.57	0.58	0.56	240	421940	241	31	157	53	172
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	32	6	16	10	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.33	9	4734	37	8	10	19	10
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...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
3PDR_A	ykoK links to Rfam database...	0.82	0.80	0.85	40	4793	9	2	5	2	10
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...	0.78	0.72	0.84	21	1508	4	2	2	0	8
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.63	0.64	0.64	21	1956	13	4	8	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.34	0.50	10	5354	27	2	8	17	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.67	0.58	0.78	14	1184	4	3	1	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.57	0.89	16	1830	2	2	0	0	12
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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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(seed) - scored higher in this pairwise comparison

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

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

Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

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