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)		HotKnots
MCC	0.640	>	0.580
Average MCC ± 95% Confidence Intervals	0.667 ± 0.075	>	0.611 ± 0.099
Sensitivity	0.491	<	0.514
Positive Predictive Value	0.839	>	0.658
Total TP	483	<	506
Total TN	198829	>	198636
Total FP	147	<	312
Total FP CONTRA	21	<	51
Total FP INCONS	72	<	212
Total FP COMP	54	>	49
Total FN	501	>	478
P-value	5.10776592382e-08

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Performance plots

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

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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	483
Total TN	198829
Total FP	147
Total FP CONTRA	21
Total FP INCONS	72
Total FP COMP	54
Total FN	501

Total Scores
MCC	0.640
Average MCC ± 95% Confidence Intervals	0.667 ± 0.075
Sensitivity	0.491
Positive Predictive Value	0.839
Nr of predictions	25

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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...	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...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	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...	0.47	0.32	0.69	42	70815	23	6	13	4	90
3IZF_C	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	6871	1	0	1	0	23
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...	0.58	0.44	0.75	12	6312	11	0	4	7	15
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	26	4	15	7	23
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	4	1	0	3	24
3O58_2	5S_rRNA links to Rfam database...	0.79	0.71	0.87	27	7229	5	2	2	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	18	2	8	8	23
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	5	0	3	2	34
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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	506
Total TN	198636
Total FP	312
Total FP CONTRA	51
Total FP INCONS	212
Total FP COMP	49
Total FN	478

Total Scores
MCC	0.580
Average MCC ± 95% Confidence Intervals	0.611 ± 0.099
Sensitivity	0.514
Positive Predictive Value	0.658
Nr of predictions	25

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2. Individual counts for HotKnots [ 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	0.65	22	7347	12	1	11	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	0.47	0.55	62	70763	52	10	41	1	70
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...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
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	0.33	10	12216	31	5	15	11	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...	0.23	0.26	0.21	9	12360	34	10	24	0	26
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.82	40	12831	11	0	9	2	32
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	6	25	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...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	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 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 HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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