CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		Vsfold5
MCC	0.593	>	0.481
Average MCC ± 95% Confidence Intervals	0.597 ± 0.088	>	0.568 ± 0.134
Sensitivity	0.397	<	0.421
Positive Predictive Value	0.887	>	0.555
Total TP	408	<	432
Total TN	236802	>	236483
Total FP	68	<	396
Total FP CONTRA	12	<	53
Total FP INCONS	40	<	294
Total FP COMP	16	<	49
Total FN	619	>	595
P-value	3.56938820447e-08

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Performance plots

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Performance of RNAalifold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	408
Total TN	236802
Total FP	68
Total FP CONTRA	12
Total FP INCONS	40
Total FP COMP	16
Total FN	619

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.597 ± 0.088
Sensitivity	0.397
Positive Predictive Value	0.887
Nr of predictions	29

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2. Individual counts for RNAalifold(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...	0.52	0.27	1.00	3	403	0	0	0	0	8
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...	0.84	0.76	0.94	16	1111	1	0	1	0	5
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.67	0.58	0.78	14	2062	4	0	4	0	10
2L1F_B	Gammaretro_CES links to Rfam database...	0.64	0.56	0.74	14	2126	5	0	5	0	11
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.59	0.35	1.00	7	4553	2	0	0	2	13
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	9	5142	0	0	0	0	33
3A3A_A	tRNA-Sec links to Rfam database...	0.71	0.51	1.00	19	3636	0	0	0	0	18
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.61	0.48	0.79	15	2327	4	2	2	0	16
3IYQ_A	tmRNA links to Rfam database...	0.38	0.21	0.69	20	60697	13	5	4	4	74
3IZ4_A	tmRNA links to Rfam database...	0.42	0.21	0.85	28	70843	5	1	4	0	104
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3LA5_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2466	3	1	2	0	18
3NPB_A	SAM links to Rfam database...	0.66	0.48	0.92	22	6997	3	1	1	1	24
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.68	0.46	1.00	33	12847	1	0	0	1	39
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	432
Total TN	236483
Total FP	396
Total FP CONTRA	53
Total FP INCONS	294
Total FP COMP	49
Total FN	595

Total Scores
MCC	0.481
Average MCC ± 95% Confidence Intervals	0.568 ± 0.134
Sensitivity	0.421
Positive Predictive Value	0.555
Nr of predictions	29

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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
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
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
3IYQ_A	tmRNA links to Rfam database...	0.33	0.31	0.35	29	60642	61	15	40	6	65
3IZ4_A	tmRNA links to Rfam database...	0.29	0.24	0.36	32	70787	62	8	49	5	100
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	32	3	19	10	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_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
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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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]