CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RSpredict(20)		Carnac(seed)
MCC	0.759	>	0.431
Average MCC ± 95% Confidence Intervals	0.762 ± 0.053	>	0.373 ± 0.095
Sensitivity	0.662	>	0.206
Positive Predictive Value	0.873	<	0.907
Total TP	934	>	291
Total TN	185178	<	185927
Total FP	202	>	70
Total FP CONTRA	10	>	4
Total FP INCONS	126	>	26
Total FP COMP	66	>	40
Total FN	477	<	1120
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RSpredict(20) and Carnac(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 RSpredict(20) and Carnac(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 RSpredict(20) and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RSpredict(20) and Carnac(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 RSpredict(20) and Carnac(seed)).

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Performance of RSpredict(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

Total Base Pair Counts
Total TP	934
Total TN	185178
Total FP	202
Total FP CONTRA	10
Total FP INCONS	126
Total FP COMP	66
Total FN	477

Total Scores
MCC	0.759
Average MCC ± 95% Confidence Intervals	0.762 ± 0.053
Sensitivity	0.662
Positive Predictive Value	0.873
Nr of predictions	68

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2. Individual counts for RSpredict(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01484	5S_rRNA links to Rfam database...	0.88	0.79	0.97	31	7471	2	0	1	1	8
CRW_01499	5S_rRNA links to Rfam database...	0.78	0.66	0.93	27	7972	2	0	2	0	14
CRW_01603	5S_rRNA links to Rfam database...	0.73	0.65	0.83	24	7111	8	0	5	3	13
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	2	0	0	2	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.56	0.49	0.65	20	5019	11	0	11	0	21
PDB_00553	mir-TAR links to Rfam database...	0.90	0.82	1.00	9	456	0	0	0	0	2
PDB_00810	s2m links to Rfam database...	0.64	0.47	0.89	8	1072	1	0	1	0	9
PDB_01050	UnaL2 links to Rfam database...	0.68	0.54	0.88	7	622	3	0	1	2	6
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	0.90	0.87	0.93	13	1417	4	0	1	3	2
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00391	Hammerhead_3 links to Rfam database...	0.83	0.80	0.86	12	1417	5	0	2	3	3
RFA_00409	Hammerhead_3 links to Rfam database...	0.83	0.80	0.86	12	1417	5	0	2	3	3
RFA_00416	Hammerhead_3 links to Rfam database...	0.87	0.87	0.87	13	1470	5	0	2	3	2
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00436	Hammerhead_3 links to Rfam database...	0.87	0.87	0.87	13	1416	5	0	2	3	2
RFA_00440	Hammerhead_3 links to Rfam database...	0.82	0.67	1.00	10	1475	3	0	0	3	5
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	7	0	0	7	0
RFA_00658	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	4	0	3	1	5
RFA_00664	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	979	4	0	3	1	6
RFA_00667	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	979	4	0	3	1	6
RFA_00668	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	982	4	0	3	1	9
RFA_00672	Hammerhead_1 links to Rfam database...	0.61	0.54	0.70	7	893	3	0	3	0	6
RFA_00673	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	4	0	3	1	7
RFA_00674	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	4	0	3	1	5
RFA_00675	Hammerhead_1 links to Rfam database...	0.62	0.50	0.78	7	981	3	0	2	1	7
RFA_00677	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00678	Hammerhead_1 links to Rfam database...	0.72	0.64	0.82	9	935	3	0	2	1	5
RFA_00680	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	4	0	3	1	4
RFA_00704	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00707	Hammerhead_1 links to Rfam database...	0.72	0.64	0.82	9	1024	3	0	2	1	5
RFA_00715	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	939	2	0	1	1	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	892	5	0	5	0	8
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	1	0	0	1	2
RFA_00731	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00733	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00734	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00736	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00737	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00745	s2m links to Rfam database...	0.91	0.83	1.00	10	936	1	0	0	1	2
RFA_00749	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00758	s2m links to Rfam database...	0.86	0.75	1.00	9	894	0	0	0	0	3
RFA_00762	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00763	s2m links to Rfam database...	0.91	0.83	1.00	10	893	1	0	0	1	2
RFA_00764	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00765	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00786	Gammaretro_CES links to Rfam database...	0.81	0.78	0.83	25	5020	5	1	4	0	7
RFA_00791	Gammaretro_CES links to Rfam database...	0.77	0.72	0.82	23	5123	6	1	4	1	9
RFA_00792	Gammaretro_CES links to Rfam database...	0.64	0.63	0.67	20	5020	11	2	8	1	12
RFA_00801	Gammaretro_CES links to Rfam database...	0.59	0.56	0.62	18	5021	12	2	9	1	14
SPR_00273	tRNA links to Rfam database...	0.90	0.90	0.90	19	2829	2	0	2	0	2
SPR_00721	tRNA links to Rfam database...	0.95	0.95	0.95	20	2905	1	0	1	0	1
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.90	0.85	0.97	28	5536	1	0	1	0	5
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.91	0.85	0.97	29	5748	1	0	1	0	5
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.84	0.74	0.96	25	5434	1	0	1	0	9
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5561	4	0	4	0	34
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.71	0.69	0.74	20	5968	8	0	7	1	9
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.72	0.56	0.92	23	6303	2	0	2	0	18
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.82	0.69	0.96	25	6877	2	0	1	1	11
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.95	0.91	1.00	31	5429	0	0	0	0	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.79	0.65	0.96	26	6759	1	0	1	0	14
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.84	0.71	1.00	27	6876	0	0	0	0	11
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.56	0.36	0.87	13	5445	2	0	2	0	23
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4751	2	1	1	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.87	0.75	1.00	27	5329	0	0	0	0	9
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6780	6	3	3	0	35

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Performance of Carnac(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	291
Total TN	185927
Total FP	70
Total FP CONTRA	4
Total FP INCONS	26
Total FP COMP	40
Total FN	1120

Total Scores
MCC	0.431
Average MCC ± 95% Confidence Intervals	0.373 ± 0.095
Sensitivity	0.206
Positive Predictive Value	0.907
Nr of predictions	68

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01484	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	39
CRW_01499	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	8001	0	0	0	0	41
CRW_01603	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...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.58	0.34	1.00	14	5036	0	0	0	0	27
PDB_00553	mir-TAR links to Rfam database...	0.79	0.64	1.00	7	458	0	0	0	0	4
PDB_00810	s2m links to Rfam database...	0.64	0.41	1.00	7	1074	0	0	0	0	10
PDB_01050	UnaL2 links to Rfam database...	0.62	0.38	1.00	5	625	1	0	0	1	8
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00391	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	2	0	0	2	2
RFA_00409	Hammerhead_3 links to Rfam database...	0.77	0.60	1.00	9	1422	1	0	0	1	6
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	4	0	1	3	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00440	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00442	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...	0.00	0.00	0.00	0	4851	0	0	0	0	15
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	985	5	1	4	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.50	0.43	0.60	6	980	4	0	4	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	1120	4	0	3	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.53	0.43	0.67	6	981	4	0	3	1	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	1118	2	0	0	2	4
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	1031	0	0	0	0	10
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	943	3	1	2	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00731	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00733	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00736	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00737	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00745	s2m links to Rfam database...	0.64	0.42	1.00	5	941	1	0	0	1	7
RFA_00749	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00758	s2m links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	12
RFA_00762	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00763	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00764	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00765	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00786	Gammaretro_CES links to Rfam database...	0.25	0.13	0.50	4	5042	4	1	3	0	28
RFA_00791	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	32
RFA_00792	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5046	4	1	3	0	32
RFA_00801	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5050	0	0	0	0	32
SPR_00273	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	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
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_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_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_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
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 RSpredict(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

2. Individual counts for RSpredict(20) [ download as .csv ]

Performance of Carnac(seed) - scored lower in this pairwise comparison

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

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