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		PPfold(seed)
MCC	0.725	>	0.626
Average MCC ± 95% Confidence Intervals	0.741 ± 0.059	>	0.464 ± 0.095
Sensitivity	0.708	>	0.495
Positive Predictive Value	0.744	<	0.794
Total TP	1978	>	1382
Total TN	1176915	<	1177832
Total FP	845	>	501
Total FP CONTRA	144	>	54
Total FP INCONS	535	>	304
Total FP COMP	166	>	143
Total FN	816	<	1412
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of IPknot and PPfold(seed). 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 PPfold(seed)).
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 PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and PPfold(seed). 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 PPfold(seed)).

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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	1978
Total TN	1176915
Total FP	845
Total FP CONTRA	144
Total FP INCONS	535
Total FP COMP	166
Total FN	816

Total Scores
MCC	0.725
Average MCC ± 95% Confidence Intervals	0.741 ± 0.059
Sensitivity	0.708
Positive Predictive Value	0.744
Nr of predictions	63

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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_01001	tRNA links to Rfam database...	0.91	0.83	1.00	15	2130	0	0	0	0	3
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00626	rne5 links to Rfam database...	0.89	0.85	0.94	74	56537	14	0	5	9	13
RFA_00627	rne5 links to Rfam database...	0.69	0.66	0.73	57	56875	35	4	17	14	30
RFA_00628	rne5 links to Rfam database...	0.95	0.90	1.00	77	57214	14	0	0	14	9
RFA_00630	rne5 links to Rfam database...	0.82	0.75	0.89	65	56880	14	0	8	6	22
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2400	15	2	13	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	3	0	3	0	10
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
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_00805	RNAIII links to Rfam database...	0.65	0.55	0.75	83	133276	35	1	26	8	67
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
RFA_00814	R2_retro_el links to Rfam database...	0.89	0.88	0.90	36	25160	11	0	4	7	5
RFA_00816	R2_retro_el links to Rfam database...	0.82	0.85	0.80	35	23176	12	8	1	3	6
RFA_00817	R2_retro_el links to Rfam database...	0.23	0.24	0.22	10	21900	38	11	24	3	31
RFA_00818	R2_retro_el links to Rfam database...	0.69	0.68	0.70	28	20261	15	9	3	3	13
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	26	0	1	25	2
SPR_00020	tRNA links to Rfam database...	0.80	0.80	0.80	16	2681	5	1	3	1	4
SPR_00137	tRNA links to Rfam database...	0.77	0.86	0.69	18	2900	13	4	4	5	3
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00394	tRNA links to Rfam database...	0.63	0.57	0.71	12	3638	5	4	1	0	9
SPR_00402	tRNA links to Rfam database...	0.79	0.62	1.00	13	2543	0	0	0	0	8
SPR_00721	tRNA links to Rfam database...	0.71	0.76	0.67	16	2902	8	2	6	0	5
SPR_00816	tRNA links to Rfam database...	0.36	0.35	0.37	7	3467	15	3	9	3	13
SPR_01157	tRNA links to Rfam database...	0.88	0.90	0.86	19	2753	4	0	3	1	2
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	30	5531	4	1	3	0	3
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	32	5743	7	1	2	4	2
SRP_00079	Plant_SRP links to Rfam database...	0.67	0.66	0.68	58	41820	33	3	24	6	30
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
SRP_00099	Plant_SRP links to Rfam database...	0.59	0.59	0.60	56	44757	38	6	31	1	39
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.96	0.94	0.97	32	5532	1	0	1	0	2
SRP_00124	Metazoa_SRP links to Rfam database...	0.86	0.81	0.92	69	37053	10	0	6	4	16
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.61	0.66	0.58	19	5962	18	3	11	4	10
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.95	0.95	0.95	39	6287	2	1	1	0	2
SRP_00182	Plant_SRP links to Rfam database...	0.75	0.73	0.76	74	45959	25	3	20	2	27
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	32	5425	3	1	2	0	2
SRP_00241	Plant_SRP links to Rfam database...	0.57	0.60	0.54	49	45965	44	12	30	2	33
SRP_00252	Metazoa_SRP links to Rfam database...	0.51	0.51	0.51	45	49053	47	7	36	4	44
SRP_00253	Metazoa_SRP links to Rfam database...	0.51	0.52	0.51	47	49362	51	9	37	5	43
SRP_00257	Metazoa_SRP links to Rfam database...	0.83	0.81	0.85	88	50937	17	4	11	2	20
SRP_00260	Metazoa_SRP links to Rfam database...	0.75	0.74	0.76	74	47798	25	4	19	2	26
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.91	0.93	0.90	37	6745	5	1	3	1	3
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.93	0.95	0.92	36	6864	3	1	2	0	2
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.95	0.93	0.97	28	3712	1	0	1	0	2
SRP_00328	Metazoa_SRP links to Rfam database...	0.65	0.65	0.66	55	39538	29	8	20	1	30
SRP_00329	Metazoa_SRP links to Rfam database...	0.63	0.61	0.65	52	39823	31	5	23	3	33
SRP_00331	Metazoa_SRP links to Rfam database...	0.52	0.53	0.51	46	37584	47	9	36	2	41
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	35	5424	1	0	1	0	1
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.57	0.51	47	41236	48	9	36	3	35
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.53	0.55	0.52	17	4720	16	0	16	0	14
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	35	5319	2	1	1	0	1

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Performance of PPfold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	1382
Total TN	1177832
Total FP	501
Total FP CONTRA	54
Total FP INCONS	304
Total FP COMP	143
Total FN	1412

Total Scores
MCC	0.626
Average MCC ± 95% Confidence Intervals	0.464 ± 0.095
Sensitivity	0.495
Positive Predictive Value	0.794
Nr of predictions	63

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	1	0	0	1	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00626	rne5 links to Rfam database...	0.94	0.89	1.00	77	56539	1	0	0	1	10
RFA_00627	rne5 links to Rfam database...	0.95	0.91	1.00	79	56874	4	0	0	4	8
RFA_00628	rne5 links to Rfam database...	0.95	0.91	1.00	78	57213	2	0	0	2	8
RFA_00630	rne5 links to Rfam database...	0.91	0.85	0.97	74	56877	5	0	2	3	13
RFA_00654	Vimentin3 links to Rfam database...	0.23	0.17	0.33	3	2406	6	0	6	0	15
RFA_00658	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1126	1	0	0	1	12
RFA_00664	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	988	1	0	0	1	12
RFA_00708	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1033	1	0	0	1	12
RFA_00749	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00764	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00765	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00767	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	1	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00805	RNAIII links to Rfam database...	0.46	0.21	1.00	32	133354	0	0	0	0	118
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...	0.50	0.38	0.67	6	2136	3	0	3	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	25164	2	0	0	2	5
RFA_00816	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	23183	2	0	0	2	4
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	1	0	0	1	4
RFA_00818	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	20265	2	0	0	2	5
RFA_00819	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	27929	2	0	0	2	4
SPR_00020	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	20
SPR_00137	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00277	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00394	tRNA links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	21
SPR_00402	tRNA links to Rfam database...	0.00	0.00	0.00	0	2556	0	0	0	0	21
SPR_00721	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00816	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	20
SPR_01157	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	21
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	33
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5778	0	0	0	0	34
SRP_00079	Plant_SRP links to Rfam database...	0.74	0.69	0.79	61	41828	28	0	16	12	27
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00099	Plant_SRP links to Rfam database...	0.60	0.59	0.62	56	44760	40	2	32	6	39
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	34
SRP_00124	Metazoa_SRP links to Rfam database...	0.71	0.66	0.76	56	37054	27	3	15	9	29
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	5995	0	0	0	0	29
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	41
SRP_00182	Plant_SRP links to Rfam database...	0.85	0.78	0.92	79	45970	17	0	7	10	22
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00241	Plant_SRP links to Rfam database...	0.53	0.52	0.54	43	45977	49	9	27	13	39
SRP_00252	Metazoa_SRP links to Rfam database...	0.64	0.63	0.64	56	49054	42	5	26	11	33
SRP_00253	Metazoa_SRP links to Rfam database...	0.64	0.62	0.66	56	49370	40	5	24	11	34
SRP_00257	Metazoa_SRP links to Rfam database...	0.51	0.44	0.59	48	50959	36	5	28	3	60
SRP_00260	Metazoa_SRP links to Rfam database...	0.56	0.51	0.61	51	47811	39	5	28	6	49
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	40
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	38
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00328	Metazoa_SRP links to Rfam database...	0.61	0.56	0.67	48	39549	29	5	19	5	37
SRP_00329	Metazoa_SRP links to Rfam database...	0.72	0.67	0.78	57	39830	26	2	14	10	28
SRP_00331	Metazoa_SRP links to Rfam database...	0.63	0.59	0.69	51	37601	31	2	21	8	36
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.50	0.59	41	41258	42	5	24	13	41
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5356	0	0	0	0	36

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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 PPfold(seed) - scored lower in this pairwise comparison

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

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