CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Cylofold		PPfold(seed)
MCC	0.624	>	0.375
Average MCC ± 95% Confidence Intervals	0.636 ± 0.099	>	0.296 ± 0.120
Sensitivity	0.593	>	0.167
Positive Predictive Value	0.661	<	0.845
Total TP	521	>	147
Total TN	121958	<	122572
Total FP	314	>	34
Total FP CONTRA	38	>	6
Total FP INCONS	229	>	21
Total FP COMP	47	>	7
Total FN	357	<	731
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	521
Total TN	121958
Total FP	314
Total FP CONTRA	38
Total FP INCONS	229
Total FP COMP	47
Total FN	357

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.636 ± 0.099
Sensitivity	0.593
Positive Predictive Value	0.661
Nr of predictions	38

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2. Individual counts for Cylofold [ 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...	0.83	0.83	0.83	15	2127	3	3	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_00654	Vimentin3 links to Rfam database...	0.26	0.22	0.31	4	2402	10	1	8	1	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	5	0	3	2	10
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...	0.48	0.42	0.56	5	894	5	1	3	1	7
RFA_00764	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	0	3	1	7
RFA_00765	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	0	3	1	7
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	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...	0.97	1.00	0.95	18	1934	1	1	0	0	0
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	3	0	0	3	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3
SPR_00020	tRNA links to Rfam database...	0.85	0.85	0.85	17	2681	5	0	3	2	3
SPR_00137	tRNA links to Rfam database...	0.84	0.86	0.82	18	2904	10	0	4	6	3
SPR_00394	tRNA links to Rfam database...	0.26	0.24	0.29	5	3638	16	5	7	4	16
SPR_00402	tRNA links to Rfam database...	1.00	1.00	1.00	21	2535	1	0	0	1	0
SPR_00721	tRNA links to Rfam database...	0.18	0.19	0.19	4	2905	17	2	15	0	17
SPR_00816	tRNA links to Rfam database...	0.34	0.35	0.33	7	3465	17	3	11	3	13
SPR_01157	tRNA links to Rfam database...	0.79	0.81	0.77	17	2753	6	4	1	1	4
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.43	0.42	0.45	14	5534	17	1	16	0	19
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.71	0.68	0.74	23	5747	10	2	6	2	11
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.59	0.59	0.61	20	5427	13	3	10	0	14
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.11	0.12	0.11	4	5529	32	2	30	0	30
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.43	0.45	0.42	13	5964	22	4	14	4	16
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.63	0.59	0.69	24	6293	11	0	11	0	17
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.62	0.59	0.67	20	5430	10	2	8	0	14
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.56	0.48	0.66	19	6757	10	0	10	0	21
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.79	0.71	0.87	27	6872	4	1	3	0	11
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.93	0.87	1.00	26	3715	0	0	0	0	4
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.61	0.56	0.67	20	5430	10	0	10	0	16
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.11	0.10	0.14	3	4732	18	1	17	0	28
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.46	0.44	0.48	16	5323	17	1	16	0	20

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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	147
Total TN	122572
Total FP	34
Total FP CONTRA	6
Total FP INCONS	21
Total FP COMP	7
Total FN	731

Total Scores
MCC	0.375
Average MCC ± 95% Confidence Intervals	0.296 ± 0.120
Sensitivity	0.167
Positive Predictive Value	0.845
Nr of predictions	38

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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_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_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 Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

2. Individual counts for Cylofold [ 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 ]