CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		PPfold(seed)
MCC	0.722	>	0.380
Average MCC ± 95% Confidence Intervals	0.698 ± 0.087	>	0.300 ± 0.117
Sensitivity	0.706	>	0.170
Positive Predictive Value	0.743	<	0.852
Total TP	646	>	156
Total TN	126818	<	127505
Total FP	290	>	34
Total FP CONTRA	34	>	6
Total FP INCONS	190	>	21
Total FP COMP	66	>	7
Total FN	269	<	759
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	646
Total TN	126818
Total FP	290
Total FP CONTRA	34
Total FP INCONS	190
Total FP COMP	66
Total FN	269

Total Scores
MCC	0.722
Average MCC ± 95% Confidence Intervals	0.698 ± 0.087
Sensitivity	0.706
Positive Predictive Value	0.743
Nr of predictions	40

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2. Individual counts for Contrafold [ 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...	0.49	0.56	0.43	10	2122	13	3	10	0	8
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	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_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...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00764	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00765	s2m links to Rfam database...	0.83	0.83	0.83	10	891	4	0	2	2	2
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	2	0	0	2	8
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	9	1	8	0	10
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...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	0	8	0	10
SPR_00020	tRNA links to Rfam database...	0.82	0.80	0.84	16	2682	6	0	3	3	4
SPR_00137	tRNA links to Rfam database...	0.84	0.86	0.82	18	2904	10	0	4	6	3
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	1	0	0	1	0
SPR_00394	tRNA links to Rfam database...	0.56	0.52	0.61	11	3637	11	5	2	4	10
SPR_00402	tRNA links to Rfam database...	0.60	0.48	0.77	10	2543	3	0	3	0	11
SPR_00721	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	2	0	0	2	0
SPR_00816	tRNA links to Rfam database...	0.31	0.35	0.28	7	3461	21	5	13	3	13
SPR_01157	tRNA links to Rfam database...	1.00	1.00	1.00	21	2754	4	0	0	4	0
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.77	0.79	0.76	26	5531	8	1	7	0	7
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.86	30	5743	9	1	4	4	4
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.78	0.79	0.77	27	5425	8	1	7	0	7
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.15	0.15	0.16	5	5534	26	2	24	0	29
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.64	0.69	0.59	20	5961	19	3	11	5	9
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.73	0.71	0.76	29	6290	10	1	8	1	12
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.84	0.85	0.83	34	6745	10	1	6	3	6
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.93	0.95	0.92	36	6864	5	1	2	2	2
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	29	3711	1	0	1	0	1
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	35	5424	2	0	1	1	1
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.47	0.48	0.45	15	4720	19	0	18	1	16
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	35	5319	3	1	1	1	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	156
Total TN	127505
Total FP	34
Total FP CONTRA	6
Total FP INCONS	21
Total FP COMP	7
Total FN	759

Total Scores
MCC	0.380
Average MCC ± 95% Confidence Intervals	0.300 ± 0.117
Sensitivity	0.170
Positive Predictive Value	0.852
Nr of predictions	40

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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_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_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
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_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	34
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_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
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_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

2. Individual counts for Contrafold [ 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 ]