CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		Carnac(seed)
MCC	0.684	>	0.260
Average MCC ± 95% Confidence Intervals	0.705 ± 0.080	>	0.160 ± 0.115
Sensitivity	0.590	>	0.068
Positive Predictive Value	0.797	<	1.000
Total TP	564	>	65
Total TN	131722	<	132365
Total FP	201	>	0
Total FP CONTRA	15	>	0
Total FP INCONS	129	>	0
Total FP COMP	57	>	0
Total FN	392	<	891
P-value	3.56938820447e-08

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Performance plots

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	564
Total TN	131722
Total FP	201
Total FP CONTRA	15
Total FP INCONS	129
Total FP COMP	57
Total FN	392

Total Scores
MCC	0.684
Average MCC ± 95% Confidence Intervals	0.705 ± 0.080
Sensitivity	0.590
Positive Predictive Value	0.797
Nr of predictions	30

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2. Individual counts for Sfold [ 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...	0.92	0.89	0.94	17	1110	2	0	1	1	2
2KUR_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KUU_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.88	0.82	0.95	18	1109	1	0	1	0	4
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...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
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...	0.45	0.35	0.58	7	1528	5	0	5	0	13
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...	0.36	0.31	0.43	13	5121	17	1	16	0	29
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...	0.72	0.55	0.96	22	4348	2	0	1	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.30	0.42	10	12222	23	3	11	9	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	19	1	10	8	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...	0.77	0.65	0.91	30	6988	6	1	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	23
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.85	40	12833	9	0	7	2	32
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...	0.65	0.50	0.84	21	3891	4	1	3	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

2. Individual counts for Sfold [ 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 ]