CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		Vsfold5
MCC	0.582	>	0.406
Average MCC ± 95% Confidence Intervals	0.536 ± 0.094	>	0.458 ± 0.126
Sensitivity	0.371	>	0.347
Positive Predictive Value	0.915	>	0.481
Total TP	396	>	370
Total TN	209673	>	209336
Total FP	59	<	451
Total FP CONTRA	8	<	52
Total FP INCONS	29	<	348
Total FP COMP	22	<	51
Total FN	670	<	696
P-value	5.19332990918e-08

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Performance plots

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Performance of Carnac(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Carnac(20)

Total Base Pair Counts
Total TP	396
Total TN	209673
Total FP	59
Total FP CONTRA	8
Total FP INCONS	29
Total FP COMP	22
Total FN	670

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.536 ± 0.094
Sensitivity	0.371
Positive Predictive Value	0.915
Nr of predictions	28

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2. Individual counts for Carnac(20) [ 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...	0.73	0.55	1.00	6	400	0	0	0	0	5
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.32	0.10	1.00	2	4558	1	0	0	1	18
2XQD_Y	tRNA links to Rfam database...	0.79	0.63	1.00	17	2833	0	0	0	0	10
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.07	1.00	3	5148	0	0	0	0	39
3A2K_C	tRNA links to Rfam database...	0.78	0.61	1.00	17	2909	0	0	0	0	11
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.57	0.33	1.00	13	4358	0	0	0	0	27
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.47	0.23	0.94	31	70843	2	0	2	0	101
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3JYV_7	tRNA links to Rfam database...	0.68	0.50	0.94	16	2833	1	0	1	0	16
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
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...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.44	0.20	1.00	9	7012	2	0	0	2	37
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
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...	0.62	0.40	0.97	29	12850	3	0	1	2	43
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
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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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	370
Total TN	209336
Total FP	451
Total FP CONTRA	52
Total FP INCONS	348
Total FP COMP	51
Total FN	696

Total Scores
MCC	0.406
Average MCC ± 95% Confidence Intervals	0.458 ± 0.126
Sensitivity	0.347
Positive Predictive Value	0.481
Nr of predictions	28

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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
2L94_A	HIV_FE links to Rfam database...	0.95	0.90	1.00	18	972	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	12	5	3	4	8
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4528	32	12	20	0	20
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5120	31	2	29	0	42
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.08	0.07	0.11	4	7344	33	0	33	0	53
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
3IZ4_A	tmRNA links to Rfam database...	0.29	0.24	0.36	32	70787	62	8	49	5	100
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.56	0.88	30	6869	4	0	4	0	24
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2831	19	0	19	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.17	0.15	0.20	4	6308	18	4	12	2	23
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_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_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
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 Carnac(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Carnac(20)

2. Individual counts for Carnac(20) [ 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 ]