CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold5		Carnac(seed)
MCC	0.503	>	0.260
Average MCC ± 95% Confidence Intervals	0.551 ± 0.130	>	0.160 ± 0.115
Sensitivity	0.437	>	0.068
Positive Predictive Value	0.585	<	1.000
Total TP	418	>	65
Total TN	131715	<	132365
Total FP	339	>	0
Total FP CONTRA	39	>	0
Total FP INCONS	258	>	0
Total FP COMP	42	>	0
Total FN	538	<	891
P-value	3.56938820447e-08

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Performance plots

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Performance of Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	418
Total TN	131715
Total FP	339
Total FP CONTRA	39
Total FP INCONS	258
Total FP COMP	42
Total FN	538

Total Scores
MCC	0.503
Average MCC ± 95% Confidence Intervals	0.551 ± 0.130
Sensitivity	0.437
Positive Predictive Value	0.585
Nr of predictions	30

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2. Individual counts for Vsfold5 [ 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...	0.90	0.82	1.00	9	397	0	0	0	0	2
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.69	0.58	0.82	14	2063	3	0	3	0	10
2L1F_B	Gammaretro_CES links to Rfam database...	0.70	0.60	0.83	15	2127	3	0	3	0	10
2L94_A	HIV_FE links to Rfam database...	0.95	0.90	1.00	18	972	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4528	32	12	20	0	20
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5120	31	2	29	0	42
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3GX2_A	SAM links to Rfam database...	0.51	0.40	0.67	16	4347	9	0	8	1	24
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	0.56	0.88	30	6869	4	0	4	0	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	32	3	19	10	23
3JYX_3	5S_rRNA links to Rfam database...	0.17	0.15	0.20	4	6308	18	4	12	2	23
3LA5_A	Purine links to Rfam database...	-0.01	0.00	0.00	0	2469	16	0	16	0	34
3NPB_A	SAM links to Rfam database...	0.57	0.46	0.72	21	6992	9	1	7	1	25
3O58_2	5S_rRNA links to Rfam database...	0.45	0.42	0.48	16	7227	19	3	14	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.37	0.41	13	12371	28	7	12	9	22
3PDR_A	ykoK links to Rfam database...	0.57	0.44	0.74	32	12837	13	0	11	2	40
3RKF_A	Purine links to Rfam database...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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 Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ 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 ]