CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MCFold		Carnac(seed)
MCC	0.534	>	0.273
Average MCC ± 95% Confidence Intervals	0.583 ± 0.118	>	0.172 ± 0.123
Sensitivity	0.554	>	0.075
Positive Predictive Value	0.521	<	1.000
Total TP	481	>	65
Total TN	120114	<	120973
Total FP	502	>	0
Total FP CONTRA	63	>	0
Total FP INCONS	380	>	0
Total FP COMP	59	>	0
Total FN	387	<	803
P-value	5.23657817852e-08

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Performance plots

Comparison of performance of MCFold and Carnac(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 MCFold and Carnac(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 MCFold and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MCFold and Carnac(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 MCFold and Carnac(seed)).

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Performance of MCFold - scored higher in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	481
Total TN	120114
Total FP	502
Total FP CONTRA	63
Total FP INCONS	380
Total FP COMP	59
Total FN	387

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.583 ± 0.118
Sensitivity	0.554
Positive Predictive Value	0.521
Nr of predictions	28

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2. Individual counts for MCFold [ 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	1	0	0	1	1
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	1109	2	0	0	2	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	21	1107	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	0.98	0.95	1.00	20	1108	1	0	0	1	1
2KUV_A	K10_TLS links to Rfam database...	0.98	0.95	1.00	21	1107	0	0	0	0	1
2KUW_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	20	1107	1	0	1	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.73	0.76	0.70	19	2118	9	0	8	1	6
2L1F_A	Gammaretro_CES links to Rfam database...	0.72	0.75	0.69	18	2054	9	0	8	1	6
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.25	0.17	5	4530	37	2	23	12	15
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.24	0.24	10	5110	32	1	30	1	32
3A3A_A	tRNA-Sec links to Rfam database...	0.89	0.86	0.91	32	3620	3	1	2	0	5
3GX2_A	SAM links to Rfam database...	0.47	0.48	0.48	19	4331	22	0	21	1	21
3IVN_B	Purine links to Rfam database...	0.39	0.39	0.40	12	2316	18	0	18	0	19
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.69	0.74	37	6853	14	0	13	1	17
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.24	0.17	8	12199	43	16	23	4	25
3JYX_3	5S_rRNA links to Rfam database...	0.41	0.52	0.33	14	6285	34	12	17	5	13
3LA5_A	Purine links to Rfam database...	0.32	0.32	0.34	11	2453	21	1	20	0	23
3O58_3	5_8S_rRNA links to Rfam database...	0.22	0.26	0.19	9	12355	45	9	30	6	26
3O58_2	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7208	44	5	38	1	29
3PDR_A	ykoK links to Rfam database...	0.66	0.61	0.72	44	12819	19	0	17	2	28
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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

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

Total Base Pair Counts
Total TP	65
Total TN	120973
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	803

Total Scores
MCC	0.273
Average MCC ± 95% Confidence Intervals	0.172 ± 0.123
Sensitivity	0.075
Positive Predictive Value	1.000
Nr of predictions	28

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2. Individual counts for Carnac(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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	19
2KUR_A	K10_TLS links to Rfam database...	0.57	0.33	1.00	7	1121	0	0	0	0	14
2KUU_A	K10_TLS links to Rfam database...	0.57	0.33	1.00	7	1121	0	0	0	0	14
2KUV_A	K10_TLS links to Rfam database...	0.64	0.41	1.00	9	1119	0	0	0	0	13
2KUW_A	K10_TLS links to Rfam database...	0.65	0.43	1.00	9	1119	0	0	0	0	12
2L1F_B	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	25
2L1F_A	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	2080	0	0	0	0	24
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.20	1.00	4	1536	0	0	0	0	16
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4560	0	0	0	0	20
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	42
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	37
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
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
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
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
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
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 MCFold - scored higher in this pairwise comparison

1. Total counts & total scores for MCFold

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

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

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

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