CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(20)		RSpredict(seed)
MCC	0.760	>	0.298
Average MCC ± 95% Confidence Intervals	0.766 ± 0.076	>	0.246 ± 0.122
Sensitivity	0.726	>	0.156
Positive Predictive Value	0.800	>	0.582
Total TP	513	>	110
Total TN	74762	<	75214
Total FP	272	>	89
Total FP CONTRA	54	>	14
Total FP INCONS	74	>	65
Total FP COMP	144	>	10
Total FN	194	<	597
P-value	5.1503931209e-08

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Performance plots

Comparison of performance of MXScarna(20) and RSpredict(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 MXScarna(20) and RSpredict(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 MXScarna(20) and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and RSpredict(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 MXScarna(20) and RSpredict(seed)).

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

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

Total Base Pair Counts
Total TP	513
Total TN	74762
Total FP	272
Total FP CONTRA	54
Total FP INCONS	74
Total FP COMP	144
Total FN	194

Total Scores
MCC	0.760
Average MCC ± 95% Confidence Intervals	0.766 ± 0.076
Sensitivity	0.726
Positive Predictive Value	0.800
Nr of predictions	27

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2. Individual counts for MXScarna(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...	0.73	0.72	0.76	13	340	5	0	4	1	5
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	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...	0.88	0.86	0.91	30	2012	4	0	3	1	5
3A2K_C	tRNA links to Rfam database...	0.74	0.73	0.76	16	1087	6	1	4	1	6
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	6	2	2	2	6
3IVN_B	Purine links to Rfam database...	0.81	0.74	0.89	17	884	2	2	0	0	6
3IZ4_A	tmRNA links to Rfam database...	0.58	0.54	0.63	51	25455	35	18	12	5	44
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	12	0	5	7	4
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_3	5S_rRNA links to Rfam database...	0.73	0.73	0.73	11	2363	26	0	4	22	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	32	5	2	25	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...	0.77	0.73	0.82	27	2245	9	2	4	3	10
3O58_2	5S_rRNA links to Rfam database...	0.92	0.90	0.93	28	2724	13	0	2	11	3
3O58_3	5_8S_rRNA links to Rfam database...	0.62	0.59	0.65	13	4744	18	5	2	11	9
3PDR_A	ykoK links to Rfam database...	0.85	0.82	0.89	41	4794	9	2	3	4	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8

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

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

Total Base Pair Counts
Total TP	110
Total TN	75214
Total FP	89
Total FP CONTRA	14
Total FP INCONS	65
Total FP COMP	10
Total FN	597

Total Scores
MCC	0.298
Average MCC ± 95% Confidence Intervals	0.246 ± 0.122
Sensitivity	0.156
Positive Predictive Value	0.582
Nr of predictions	27

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2. Individual counts for RSpredict(seed) [ 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...	0.89	0.80	1.00	8	166	0	0	0	0	2
2L94_A	HIV_FE links to Rfam database...	0.55	0.50	0.64	9	343	6	0	5	1	9
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	1150	3	1	1	1	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.36	0.40	4	1825	8	4	2	2	7
2XQD_Y	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1124	5	0	5	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.20	0.70	7	2035	3	0	3	0	28
3A2K_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1106	2	0	2	0	22
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3GX2_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1442	1	0	1	0	22
3IVN_B	Purine links to Rfam database...	0.81	0.70	0.94	16	886	1	1	0	0	7
3IZ4_A	tmRNA links to Rfam database...	0.26	0.11	0.63	10	25520	7	2	4	1	85
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2635	5	0	5	0	35
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	4	0	3	1	20
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2373	5	1	4	0	15
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4754	5	0	2	3	12
3LA5_A	Purine links to Rfam database...	0.82	0.68	1.00	17	937	0	0	0	0	8
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2274	4	0	4	0	37
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2751	3	0	3	0	31
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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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 MXScarna(20) - scored higher in this pairwise comparison

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

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

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

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

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