CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		Mastr(seed)
MCC	0.533	>	0.000
Average MCC ± 95% Confidence Intervals	0.567 ± 0.078	>	0.000 ± 0.000
Sensitivity	0.472	>	0.000
Positive Predictive Value	0.606	>	0.000
Total TP	630	>	0
Total TN	283091	<	284130
Total FP	483	>	0
Total FP CONTRA	63	>	0
Total FP INCONS	346	>	0
Total FP COMP	74	>	0
Total FN	705	<	1335
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAshapes and Mastr(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 RNAshapes and Mastr(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 RNAshapes and Mastr(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and Mastr(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 RNAshapes and Mastr(seed)).

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	630
Total TN	283091
Total FP	483
Total FP CONTRA	63
Total FP INCONS	346
Total FP COMP	74
Total FN	705

Total Scores
MCC	0.533
Average MCC ± 95% Confidence Intervals	0.567 ± 0.078
Sensitivity	0.472
Positive Predictive Value	0.606
Nr of predictions	35

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2. Individual counts for RNAshapes [ 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
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2WRQ_Y	tRNA links to Rfam database...	0.59	0.59	0.59	10	2833	12	4	3	5	7
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XQD_Y	tRNA links to Rfam database...	0.64	0.56	0.75	15	2830	5	0	5	0	12
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.12	3	3460	23	0	23	0	29
2ZZN_D	tRNA links to Rfam database...	0.69	0.63	0.77	17	2463	5	1	4	0	10
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.76	0.65	0.89	24	3628	3	0	3	0	13
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
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...	0.41	0.32	0.53	18	7347	16	1	15	0	39
3GX2_A	SAM links to Rfam database...	0.76	0.63	0.93	25	4344	3	0	2	1	15
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IYQ_A	tmRNA links to Rfam database...	0.26	0.28	0.24	26	60619	83	21	60	2	68
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.60	60	70776	45	6	34	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.68	28	6862	13	1	12	0	26
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
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...	0.77	0.63	0.94	29	6990	4	1	1	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3O58_2	5S_rRNA links to Rfam database...	0.60	0.61	0.59	23	7221	18	4	12	2	15
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.80	40	12830	12	0	10	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
3UZL_B	tRNA links to Rfam database...	0.39	0.32	0.48	12	3545	13	2	11	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	5	25	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
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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Performance of Mastr(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	0
Total TN	284130
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	1335

Total Scores
MCC	0.000
Average MCC ± 95% Confidence Intervals	0.000 ± 0.000
Sensitivity	0.000
Positive Predictive Value	0.000
Nr of predictions	35

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2. Individual counts for Mastr(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...	0.00	0.00	0.00	0	406	0	0	0	0	11
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	17
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	27
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32
2ZZN_D	tRNA links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	27
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	37
3AKZ_H	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	28
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3G4S_9	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7381	0	0	0	0	57
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	40
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	2346	0	0	0	0	31
3IYQ_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	60726	0	0	0	0	94
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	70876	0	0	0	0	132
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	33
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	27
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	34
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

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

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

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

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