CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAsubopt		Carnac(seed)
MCC	0.636	>	0.260
Average MCC ± 95% Confidence Intervals	0.657 ± 0.096	>	0.160 ± 0.115
Sensitivity	0.575	>	0.068
Positive Predictive Value	0.708	<	1.000
Total TP	550	>	65
Total TN	131653	<	132365
Total FP	284	>	0
Total FP CONTRA	35	>	0
Total FP INCONS	192	>	0
Total FP COMP	57	>	0
Total FN	406	<	891
P-value	3.56938820447e-08

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Performance plots

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Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	550
Total TN	131653
Total FP	284
Total FP CONTRA	35
Total FP INCONS	192
Total FP COMP	57
Total FN	406

Total Scores
MCC	0.636
Average MCC ± 95% Confidence Intervals	0.657 ± 0.096
Sensitivity	0.575
Positive Predictive Value	0.708
Nr of predictions	30

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2. Individual counts for RNAsubopt [ 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...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	2059	0	0	0	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.94	0.88	1.00	22	2123	0	0	0	0	3
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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.47	0.43	0.53	18	5117	16	1	15	0	24
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3GX2_A	SAM links to Rfam database...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.21	0.17	7	12204	38	11	24	3	26
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...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.75	0.65	0.86	30	6986	7	1	4	2	16
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	28	7220	13	4	8	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
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	0	7	0	14

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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	132365
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	891

Total Scores
MCC	0.260
Average MCC ± 95% Confidence Intervals	0.160 ± 0.115
Sensitivity	0.068
Positive Predictive Value	1.000
Nr of predictions	30

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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_A	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	2080	0	0	0	0	24
2L1F_B	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	25
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
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
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_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 RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

2. Individual counts for RNAsubopt [ 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 ]