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)		Murlet(20)
MCC	0.755	>	0.693
Average MCC ± 95% Confidence Intervals	0.762 ± 0.067	>	0.690 ± 0.070
Sensitivity	0.720	>	0.594
Positive Predictive Value	0.796	<	0.815
Total TP	645	>	532
Total TN	92052	<	92209
Total FP	335	>	202
Total FP CONTRA	65	>	25
Total FP INCONS	100	>	96
Total FP COMP	170	>	81
Total FN	251	<	364
P-value	3.56938820447e-08

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Performance plots

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

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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	645
Total TN	92052
Total FP	335
Total FP CONTRA	65
Total FP INCONS	100
Total FP COMP	170
Total FN	251

Total Scores
MCC	0.755
Average MCC ± 95% Confidence Intervals	0.762 ± 0.067
Sensitivity	0.720
Positive Predictive Value	0.796
Nr of predictions	34

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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
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	16	2	3	11	6
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
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J20_1	tRNA links to Rfam database...	0.97	0.95	1.00	19	1093	1	0	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.67	0.65	0.71	22	2989	11	3	6	2	12
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	32	5	2	25	2
3JYX_3	5S_rRNA links to Rfam database...	0.73	0.73	0.73	11	2363	26	0	4	22	4
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2763	13	0	4	9	6
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

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

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

Total Base Pair Counts
Total TP	532
Total TN	92209
Total FP	202
Total FP CONTRA	25
Total FP INCONS	96
Total FP COMP	81
Total FN	364

Total Scores
MCC	0.693
Average MCC ± 95% Confidence Intervals	0.690 ± 0.070
Sensitivity	0.594
Positive Predictive Value	0.815
Nr of predictions	34

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2. Individual counts for Murlet(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...	0.70	0.50	1.00	5	169	0	0	0	0	5
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	0.63	0.67	0.60	6	1142	13	1	3	9	3
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...	0.88	0.86	0.90	18	1109	3	0	2	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.88	0.86	0.90	19	1087	2	0	2	0	3
3AMU_B	tRNA links to Rfam database...	0.89	0.89	0.89	17	1138	4	0	2	2	2
3G4S_9	5S_rRNA links to Rfam database...	0.85	0.77	0.95	20	2715	5	0	1	4	6
3GX2_A	SAM links to Rfam database...	0.73	0.54	1.00	15	1434	1	0	0	1	13
3IVN_B	Purine links to Rfam database...	0.80	0.65	1.00	15	888	0	0	0	0	8
3IZ4_A	tmRNA links to Rfam database...	0.46	0.33	0.66	31	25489	22	3	13	6	64
3IZF_C	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2609	5	0	2	3	6
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J20_1	tRNA links to Rfam database...	0.69	0.60	0.80	12	1097	4	0	3	1	8
3J2L_3	5S_rRNA links to Rfam database...	0.84	0.74	0.96	25	2994	4	0	1	3	9
3JYV_7	tRNA links to Rfam database...	0.84	0.80	0.89	16	1093	4	0	2	2	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.72	0.75	0.69	9	4743	15	3	1	11	3
3JYX_3	5S_rRNA links to Rfam database...	0.76	0.73	0.79	11	2364	14	0	3	11	4
3LA5_A	Purine links to Rfam database...	0.80	0.64	1.00	16	938	0	0	0	0	9
3NPB_A	SAM links to Rfam database...	0.65	0.43	1.00	16	2262	2	0	0	2	21
3O58_2	5S_rRNA links to Rfam database...	1.00	1.00	1.00	31	2723	2	0	0	2	0
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	3	1	2	0	12
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.38	0.48	11	5351	16	2	10	4	18
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	5	0	2	3	5
4A1C_3	5S_rRNA links to Rfam database...	0.72	0.59	0.88	22	2738	4	0	3	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
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...	0.19	0.17	0.25	4	1186	12	1	11	0	20

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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 Murlet(20) - scored lower in this pairwise comparison

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

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