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)		Mastr(seed)
MCC	0.798	>	0.330
Average MCC ± 95% Confidence Intervals	0.772 ± 0.086	>	0.272 ± 0.123
Sensitivity	0.766	>	0.154
Positive Predictive Value	0.835	>	0.714
Total TP	546	>	110
Total TN	103068	<	103568
Total FP	160	>	53
Total FP CONTRA	22	>	8
Total FP INCONS	86	>	36
Total FP COMP	52	>	9
Total FN	167	<	603
P-value	3.56938820447e-08

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Performance plots

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

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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	546
Total TN	103068
Total FP	160
Total FP CONTRA	22
Total FP INCONS	86
Total FP COMP	52
Total FN	167

Total Scores
MCC	0.798
Average MCC ± 95% Confidence Intervals	0.772 ± 0.086
Sensitivity	0.766
Positive Predictive Value	0.835
Nr of predictions	33

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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_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...	0.38	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 Mastr(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	110
Total TN	103568
Total FP	53
Total FP CONTRA	8
Total FP INCONS	36
Total FP COMP	9
Total FN	603

Total Scores
MCC	0.330
Average MCC ± 95% Confidence Intervals	0.272 ± 0.123
Sensitivity	0.154
Positive Predictive Value	0.714
Nr of predictions	33

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2. Individual counts for Mastr(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...	0.00	0.00	0.00	0	7140	0	0	0	0	37
PDB_00012	mir-TAR links to Rfam database...	0.00	0.00	0.00	0	406	0	0	0	0	7
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00416	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00433	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00587	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4851	0	0	0	0	15
RFA_00636	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	28
RFA_00654	Vimentin3 links to Rfam database...	0.62	0.39	1.00	7	2408	0	0	0	0	11
RFA_00658	Hammerhead_1 links to Rfam database...	0.56	0.43	0.75	6	1120	3	0	2	1	8
RFA_00664	Hammerhead_1 links to Rfam database...	0.27	0.07	1.00	1	989	0	0	0	0	13
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4270	8	3	5	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.21	0.75	3	1031	1	0	1	0	11
RFA_00749	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00764	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00765	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00767	Corona_pk3 links to Rfam database...	0.67	0.50	0.90	9	1881	1	0	1	0	9
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...	0.64	0.50	0.82	9	1942	2	1	1	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	1942	2	1	1	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	17	2	13	2	16
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	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_00137	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	25
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5253	0	0	0	0	36
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	36
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
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_00357	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5356	0	0	0	0	36
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	35

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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 Mastr(seed) - scored lower in this pairwise comparison

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

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