CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		HotKnots
MCC	0.489	>	0.453
Average MCC ± 95% Confidence Intervals	0.564 ± 0.083	>	0.555 ± 0.100
Sensitivity	0.435	<	0.445
Positive Predictive Value	0.556	>	0.469
Total TP	513	<	524
Total TN	158584	>	158389
Total FP	421	<	609
Total FP CONTRA	53	<	81
Total FP INCONS	356	<	512
Total FP COMP	12	<	16
Total FN	665	>	654
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of IPknot and HotKnots. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for IPknot and HotKnots).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for IPknot and HotKnots).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and HotKnots. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for IPknot and HotKnots).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	513
Total TN	158584
Total FP	421
Total FP CONTRA	53
Total FP INCONS	356
Total FP COMP	12
Total FN	665

Total Scores
MCC	0.489
Average MCC ± 95% Confidence Intervals	0.564 ± 0.083
Sensitivity	0.435
Positive Predictive Value	0.556
Nr of predictions	53

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.71	0.71	0.71	10	932	4	0	4	0	4
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.41	0.35	0.50	7	766	7	0	7	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	0.17	0.20	0.18	2	485	9	2	7	0	8
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	0.76	0.58	1.00	7	623	0	0	0	0	5
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00370	-	0.00	0.00	0.00	0	15225	0	0	0	0	25
PDB_00447	-	0.41	0.25	0.69	11	7124	5	0	5	0	33
PDB_00571	tRNA links to Rfam database...	0.79	0.76	0.83	19	3298	4	2	2	0	6
PDB_00713	-	0.52	0.43	0.64	9	2002	5	0	5	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	21	0	21	0	23
PDB_00804	-	0.23	0.24	0.23	12	15348	42	10	30	2	38
PDB_00828	Purine links to Rfam database...	0.90	0.81	1.00	22	2463	0	0	0	0	5
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.45	0.39	0.53	16	4723	14	0	14	0	25
PDB_00857	-	0.93	0.87	1.00	13	1068	0	0	0	0	2
PDB_00874	-	0.10	0.10	0.13	2	931	13	2	11	0	18
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.71	0.81	0.63	17	2458	10	5	5	0	4
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.32	0.26	0.40	14	12685	21	0	21	0	40
PDB_01073	SAM links to Rfam database...	0.80	0.65	1.00	22	4349	1	0	0	1	12
PDB_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01194	-	0.52	0.33	0.83	5	490	1	1	0	0	10
PDB_01201	-	0.61	0.45	0.83	10	1116	2	0	2	0	12
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.18	0.15	0.22	6	12063	21	5	16	0	35
PDB_01260	-	0.58	0.48	0.71	12	1813	5	1	4	0	13
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.71	0.67	0.77	10	890	3	2	1	0	5
PDB_01309	-	-0.01	0.00	0.00	0	9118	62	9	53	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.42	0.36	0.50	10	4075	11	0	10	1	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	3	6	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	2005	4	0	2	2	9
RFA_00773	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	8	1	4	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	4	0	4	0	10

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	524
Total TN	158389
Total FP	609
Total FP CONTRA	81
Total FP INCONS	512
Total FP COMP	16
Total FN	654

Total Scores
MCC	0.453
Average MCC ± 95% Confidence Intervals	0.555 ± 0.100
Sensitivity	0.445
Positive Predictive Value	0.469
Nr of predictions	53

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.38	0.35	0.44	7	764	9	0	9	0	13
PDB_00041	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00053	-	1.00	1.00	1.00	11	424	0	0	0	0	0
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	0.71	0.58	0.88	7	622	1	0	1	0	5
PDB_00352	-	0.89	0.79	1.00	15	1210	0	0	0	0	4
PDB_00370	-	0.09	0.12	0.07	3	15179	45	12	31	2	22
PDB_00447	-	0.23	0.23	0.25	10	7100	30	6	24	0	34
PDB_00571	tRNA links to Rfam database...	0.17	0.16	0.19	4	3300	17	6	11	0	21
PDB_00713	-	0.43	0.43	0.45	9	1996	11	0	11	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2678	24	1	22	1	23
PDB_00804	-	0.22	0.24	0.21	12	15342	48	10	36	2	38
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_00857	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	0.10	0.10	0.14	2	932	12	2	10	0	18
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.52	0.57	0.48	12	2460	13	5	8	0	9
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.33	6	1110	12	0	12	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.31	0.30	0.33	16	12671	33	2	31	0	38
PDB_01073	SAM links to Rfam database...	0.81	0.74	0.89	25	4343	4	2	1	1	9
PDB_01092	glmS links to Rfam database...	0.69	0.65	0.74	34	10107	13	0	12	1	18
PDB_01194	-	0.93	0.93	0.93	14	481	1	1	0	0	1
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.71	0.63	0.80	12	1161	3	2	1	0	7
PDB_01250	-	0.10	0.10	0.12	4	12056	30	7	23	0	37
PDB_01260	-	0.41	0.36	0.47	9	1811	10	0	10	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.74	0.67	0.83	10	891	2	1	1	0	5
PDB_01309	-	-0.01	0.00	0.00	0	9118	62	9	53	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	2	17	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1870	3	3	0	0	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	21	0	19	2	18
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1999	20	0	17	3	18
RFA_00773	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	22	0	19	3	18
RFA_00779	Corona_pk3 links to Rfam database...	0.87	0.94	0.81	17	1932	4	3	1	0	1
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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