CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		Mastr(20)
MCC	0.686	>	0.620
Average MCC ± 95% Confidence Intervals	0.650 ± 0.095	>	0.584 ± 0.128
Sensitivity	0.518	>	0.473
Positive Predictive Value	0.915	>	0.819
Total TP	464	>	424
Total TN	92355	>	92344
Total FP	102	<	174
Total FP CONTRA	8	<	16
Total FP INCONS	35	<	78
Total FP COMP	59	<	80
Total FN	432	<	472
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	424
Total TN	92344
Total FP	174
Total FP CONTRA	16
Total FP INCONS	78
Total FP COMP	80
Total FN	472

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.584 ± 0.128
Sensitivity	0.473
Positive Predictive Value	0.819
Nr of predictions	34

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2. Individual counts for Mastr(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...	0.88	0.83	0.94	15	341	2	0	1	1	3
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	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...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.81	0.77	0.85	17	1088	3	0	3	0	5
3AMU_B	tRNA links to Rfam database...	0.89	0.79	1.00	15	1142	2	0	0	2	4
3G4S_9	5S_rRNA links to Rfam database...	0.68	0.62	0.76	16	2715	10	2	3	5	10
3GX2_A	SAM links to Rfam database...	0.46	0.39	0.55	11	1429	10	2	7	1	17
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	25536	0	0	0	0	95
3IZF_C	5S_rRNA links to Rfam database...	0.91	0.91	0.91	32	2605	9	0	3	6	3
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	0.26	0.25	0.29	5	1095	12	1	11	0	15
3J2L_3	5S_rRNA links to Rfam database...	0.42	0.38	0.48	13	2993	16	2	12	2	21
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...	0.00	0.00	0.00	0	4756	0	0	0	0	12
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
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...	0.34	0.30	0.41	11	2251	18	1	15	2	26
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	12	0	2	10	2
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.71	1.00	17	849	0	0	0	0	7
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	5374	0	0	0	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	7	0	2	5	3
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.42	0.34	0.53	10	1418	10	1	8	1	19
4ENB_A	crcB links to Rfam database...	0.44	0.20	1.00	3	469	0	0	0	0	12
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...	0.00	0.00	0.00	0	1202	0	0	0	0	24

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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 Carnac(20) - scored higher in this pairwise comparison

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

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

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

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

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