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)		Carnac(20)
MCC	0.751	>	0.686
Average MCC ± 95% Confidence Intervals	0.774 ± 0.073	>	0.650 ± 0.095
Sensitivity	0.663	>	0.518
Positive Predictive Value	0.856	<	0.915
Total TP	594	>	464
Total TN	92168	<	92355
Total FP	209	>	102
Total FP CONTRA	41	>	8
Total FP INCONS	59	>	35
Total FP COMP	109	>	59
Total FN	302	<	432
P-value	3.56938820447e-08

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Performance plots

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

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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	594
Total TN	92168
Total FP	209
Total FP CONTRA	41
Total FP INCONS	59
Total FP COMP	109
Total FN	302

Total Scores
MCC	0.751
Average MCC ± 95% Confidence Intervals	0.774 ± 0.073
Sensitivity	0.663
Positive Predictive Value	0.856
Nr of predictions	34

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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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
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	2	0	0	2	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...	0.34	0.11	1.00	4	2041	0	0	0	0	31
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3G4S_9	5S_rRNA links to Rfam database...	0.73	0.54	1.00	14	2722	4	0	0	4	12
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...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2610	2	0	0	2	5
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	26	10	2	14	2
3JYX_3	5S_rRNA links to Rfam database...	0.70	0.60	0.82	9	2367	14	0	2	12	6
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	5	0	0	5	4
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
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...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

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Performance of Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	464
Total TN	92355
Total FP	102
Total FP CONTRA	8
Total FP INCONS	35
Total FP COMP	59
Total FN	432

Total Scores
MCC	0.686
Average MCC ± 95% Confidence Intervals	0.650 ± 0.095
Sensitivity	0.518
Positive Predictive Value	0.915
Nr of predictions	34

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2. Individual counts for Carnac(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...	0.77	0.60	1.00	6	168	0	0	0	0	4
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	357	0	0	0	0	18
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...	0.43	0.18	1.00	2	1833	1	0	0	1	9
2XQD_Y	tRNA links to Rfam database...	0.87	0.76	1.00	16	1113	1	0	0	1	5
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.29	0.09	1.00	3	2042	0	0	0	0	32
3A2K_C	tRNA links to Rfam database...	0.88	0.77	1.00	17	1091	0	0	0	0	5
3AMU_B	tRNA links to Rfam database...	0.79	0.79	0.79	15	1138	7	0	4	3	4
3G4S_9	5S_rRNA links to Rfam database...	0.73	0.54	1.00	14	2722	4	0	0	4	12
3GX2_A	SAM links to Rfam database...	0.68	0.46	1.00	13	1436	0	0	0	0	15
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.31	0.88	29	25503	4	3	1	0	66
3IZF_C	5S_rRNA links to Rfam database...	0.91	0.83	1.00	29	2611	2	0	0	2	6
3J20_0	tRNA links to Rfam database...	0.69	0.71	0.68	15	1197	8	1	6	1	6
3J20_1	tRNA links to Rfam database...	0.89	0.80	1.00	16	1096	1	0	0	1	4
3J2L_3	5S_rRNA links to Rfam database...	0.59	0.53	0.67	18	2993	11	0	9	2	16
3JYV_7	tRNA links to Rfam database...	0.81	0.70	0.93	14	1096	3	0	1	2	6
3JYX_4	5_8S_rRNA links to Rfam database...	0.76	0.58	1.00	7	4749	2	0	0	2	5
3JYX_3	5S_rRNA links to Rfam database...	0.83	0.80	0.86	12	2364	13	0	2	11	3
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...	0.46	0.22	1.00	8	2270	3	0	0	3	29
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	2	0	0	2	4
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...	0.75	0.58	0.97	29	4810	3	1	0	2	21
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.21	0.67	6	5365	4	1	2	1	23
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.66	1.00	23	2773	3	0	0	3	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.42	0.25	0.71	5	4509	3	0	2	1	15
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	14	1418	6	2	3	1	15
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.50	0.25	1.00	6	1196	0	0	0	0	18

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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 Carnac(20) - scored lower in this pairwise comparison

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

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