CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	NanoFolder		Mastr(seed)
MCC	0.369	>	0.191
Average MCC ± 95% Confidence Intervals	0.396 ± 0.076	>	0.126 ± 0.079
Sensitivity	0.424	>	0.055
Positive Predictive Value	0.330	<	0.673
Total TP	510	>	66
Total TN	185207	<	186655
Total FP	1111	>	40
Total FP CONTRA	202	>	6
Total FP INCONS	834	>	26
Total FP COMP	75	>	8
Total FN	693	<	1137
P-value	3.56938820447e-08

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Performance plots

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

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Performance of NanoFolder - scored higher in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	510
Total TN	185207
Total FP	1111
Total FP CONTRA	202
Total FP INCONS	834
Total FP COMP	75
Total FN	693

Total Scores
MCC	0.369
Average MCC ± 95% Confidence Intervals	0.396 ± 0.076
Sensitivity	0.424
Positive Predictive Value	0.330
Nr of predictions	49

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2. Individual counts for NanoFolder [ 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...	0.20	0.24	0.17	9	7088	43	7	36	0	28
CRW_01590	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	7093	50	7	40	3	37
CRW_01603	5S_rRNA links to Rfam database...	0.41	0.46	0.38	17	7095	29	6	22	1	20
PDB_00070	tRNA links to Rfam database...	0.25	0.29	0.23	7	2819	24	4	20	0	17
PDB_00828	Purine links to Rfam database...	0.30	0.33	0.28	9	2453	23	0	23	0	18
PDB_01051	Telomerase-cil links to Rfam database...	-0.02	0.00	0.00	0	885	18	1	17	0	13
PDB_01236	ykoK links to Rfam database...	0.31	0.33	0.30	18	11568	43	3	39	1	36
RFA_00416	Hammerhead_3 links to Rfam database...	0.94	1.00	0.88	15	1468	6	2	0	4	0
RFA_00434	Hammerhead_3 links to Rfam database...	0.84	1.00	0.71	15	1410	8	6	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	0.86	1.00	0.75	15	1411	7	5	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	0.94	1.00	0.88	15	1414	4	2	0	2	0
RFA_00446	Hammerhead_3 links to Rfam database...	0.85	0.93	0.78	14	1467	7	3	1	3	1
RFA_00604	Telomerase-cil links to Rfam database...	0.42	0.54	0.33	19	13472	53	14	25	14	16
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	978	13	0	12	1	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.12	0.14	0.13	2	1112	15	0	14	1	12
RFA_00675	Hammerhead_1 links to Rfam database...	0.28	0.29	0.29	4	976	10	1	9	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.62	0.64	0.60	9	975	10	0	6	4	5
RFA_00684	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	977	5	2	1	2	4
RFA_00703	Hammerhead_1 links to Rfam database...	0.26	0.36	0.19	5	4252	32	5	16	11	9
RFA_00716	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	929	17	0	17	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	889	5	2	3	0	5
RFA_00730	s2m links to Rfam database...	0.38	0.42	0.36	5	889	10	3	6	1	7
RFA_00763	s2m links to Rfam database...	0.38	0.42	0.36	5	889	10	3	6	1	7
RFA_00765	s2m links to Rfam database...	0.39	0.42	0.38	5	890	9	2	6	1	7
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1996	24	0	20	4	18
RFA_00773	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1932	9	3	0	6	0
RFA_00808	RydC links to Rfam database...	0.83	1.00	0.70	16	1993	7	7	0	0	0
SPR_00314	tRNA links to Rfam database...	0.47	0.57	0.39	12	2895	21	9	10	2	9
SPR_00452	tRNA links to Rfam database...	0.27	0.33	0.23	7	2820	24	7	16	1	14
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.23	0.27	0.20	9	5005	36	1	35	0	24
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.33	0.38	0.29	12	4712	30	3	26	1	20
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.29	0.36	0.25	9	4059	28	4	23	1	16
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.27	0.33	0.23	7	3209	27	5	19	3	14
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.41	0.47	0.35	17	6855	31	4	27	0	19
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.44	0.48	0.41	13	3371	19	4	15	0	14
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.42	0.52	0.35	14	5213	26	8	18	0	13
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.25	0.30	0.22	10	5106	35	4	31	0	23
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.47	0.55	0.40	17	5109	25	7	18	0	14
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.38	0.44	0.34	17	6853	33	2	31	0	22
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.66	0.46	19	4615	22	8	14	0	10
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.46	0.52	0.43	17	5010	24	6	17	1	16
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.36	0.40	0.33	16	6737	34	6	27	1	24
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.38	0.43	0.35	13	3704	24	6	18	0	17
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.36	0.41	0.33	13	6630	27	3	24	0	19
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.20	0.24	0.19	8	5108	35	3	32	0	26
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.52	0.56	0.49	20	5419	22	4	17	1	16
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.20	0.24	0.17	6	3970	29	7	22	0	19
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.32	0.37	0.28	13	6282	33	4	29	0	22
SRP_00383	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3205	35	9	26	0	24

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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	66
Total TN	186655
Total FP	40
Total FP CONTRA	6
Total FP INCONS	26
Total FP COMP	8
Total FN	1137

Total Scores
MCC	0.191
Average MCC ± 95% Confidence Intervals	0.126 ± 0.079
Sensitivity	0.055
Positive Predictive Value	0.673
Nr of predictions	49

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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
CRW_01590	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	37
CRW_01603	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	37
PDB_00070	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	24
PDB_00828	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	27
PDB_01051	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
PDB_01236	ykoK links to Rfam database...	0.00	0.00	0.00	0	11628	0	0	0	0	54
RFA_00416	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00434	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00436	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00442	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00446	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00604	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00664	Hammerhead_1 links to Rfam database...	0.27	0.07	1.00	1	989	0	0	0	0	13
RFA_00674	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	1124	0	0	0	0	10
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	989	1	0	1	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.46	0.21	1.00	3	987	0	0	0	0	11
RFA_00684	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4270	8	3	5	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	0.26	0.14	0.50	2	942	2	0	2	0	12
RFA_00717	Hammerhead_1 links to Rfam database...	0.62	0.50	0.78	7	894	2	0	2	0	7
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00763	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_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_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	17	2	13	2	16
SPR_00314	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00452	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5050	0	0	0	0	33
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	32
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	25
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3240	0	0	0	0	21
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	36
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3403	0	0	0	0	27
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5253	0	0	0	0	27
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	33
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	31
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	39
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4656	0	0	0	0	29
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5050	0	0	0	0	33
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	40
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6670	0	0	0	0	32
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	34
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	25
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	35
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3240	0	0	0	0	24

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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 NanoFolder - scored higher in this pairwise comparison

1. Total counts & total scores for NanoFolder

2. Individual counts for NanoFolder [ 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 ]