CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	TurboFold(seed)		Cylofold
MCC	0.800	>	0.653
Average MCC ± 95% Confidence Intervals	0.772 ± 0.089	>	0.671 ± 0.102
Sensitivity	0.770	>	0.626
Positive Predictive Value	0.833	>	0.686
Total TP	537	>	436
Total TN	101061	<	101070
Total FP	160	<	245
Total FP CONTRA	22	<	34
Total FP INCONS	86	<	166
Total FP COMP	52	>	45
Total FN	160	<	261
P-value	3.56938820447e-08

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Performance plots

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

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Performance of TurboFold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	537
Total TN	101061
Total FP	160
Total FP CONTRA	22
Total FP INCONS	86
Total FP COMP	52
Total FN	160

Total Scores
MCC	0.800
Average MCC ± 95% Confidence Intervals	0.772 ± 0.089
Sensitivity	0.770
Positive Predictive Value	0.833
Nr of predictions	32

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01535	5S_rRNA links to Rfam database...	0.94	0.89	1.00	33	7107	3	0	0	3	4
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
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	2	0	0	2	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	11	0	0	11	0
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00654	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2405	5	1	3	1	12
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_00703	Hammerhead_1 links to Rfam database...	0.67	0.64	0.69	9	4265	18	1	3	14	5
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...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	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	2	1	0	1	8
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	0	1	0	8
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	9	1	8	0	10
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.88	0.88	0.88	30	5426	4	1	3	0	4
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.61	0.66	0.58	19	5962	18	3	11	4	10
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.75	0.84	0.68	21	4155	10	4	6	0	4
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5216	3	1	2	0	2
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.90	0.92	0.89	33	6866	4	1	3	0	3
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.91	0.91	0.91	31	5426	3	1	2	0	3
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.95	0.93	0.97	28	3712	1	0	1	0	2
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.94	0.94	0.94	34	5424	2	0	2	0	2
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5319	3	1	2	0	2
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	33	6750	3	1	2	0	2

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	436
Total TN	101070
Total FP	245
Total FP CONTRA	34
Total FP INCONS	166
Total FP COMP	45
Total FN	261

Total Scores
MCC	0.653
Average MCC ± 95% Confidence Intervals	0.671 ± 0.102
Sensitivity	0.626
Positive Predictive Value	0.686
Nr of predictions	32

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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
CRW_01535	5S_rRNA links to Rfam database...	0.40	0.38	0.42	14	7107	21	2	17	2	23
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
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_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	8	0	0	8	0
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.82	0.74	23	3974	8	7	1	0	5
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_00703	Hammerhead_1 links to Rfam database...	0.30	0.36	0.25	5	4258	19	4	11	4	9
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
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.59	0.59	0.61	20	5427	13	3	10	0	14
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.43	0.45	0.42	13	5964	22	4	14	4	16
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.59	0.52	0.68	13	4167	6	2	4	0	12
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.33	0.33	0.34	12	5218	23	4	19	0	24
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.61	0.56	0.67	20	6873	10	1	9	0	16
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.62	0.59	0.67	20	5430	10	2	8	0	14
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_00357	Bacteria_small_SRP links to Rfam database...	0.46	0.44	0.48	16	5323	17	1	16	0	20
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.69	0.69	0.71	24	6752	10	0	10	0	11

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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 TurboFold(seed) - scored higher in this pairwise comparison

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

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

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

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