CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		Mastr(20)
MCC	0.815	>	0.659
Average MCC ± 95% Confidence Intervals	0.825 ± 0.025	>	0.680 ± 0.042
Sensitivity	0.743	>	0.520
Positive Predictive Value	0.897	>	0.839
Total TP	2484	>	1741
Total TN	500887	<	501582
Total FP	552	>	542
Total FP CONTRA	38	<	48
Total FP INCONS	247	<	285
Total FP COMP	267	>	209
Total FN	861	<	1604
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(seed) and Mastr(20). 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 CentroidAlifold(seed) and Mastr(20)).
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 CentroidAlifold(seed) and Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Mastr(20). 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 CentroidAlifold(seed) and Mastr(20)).

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

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

Total Base Pair Counts
Total TP	2484
Total TN	500887
Total FP	552
Total FP CONTRA	38
Total FP INCONS	247
Total FP COMP	267
Total FN	861

Total Scores
MCC	0.815
Average MCC ± 95% Confidence Intervals	0.825 ± 0.025
Sensitivity	0.743
Positive Predictive Value	0.897
Nr of predictions	141

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.85	0.73	1.00	30	5020	0	0	0	0	11
PDB_00553	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	455	0	0	0	0	1
PDB_00741	Entero_5_CRE links to Rfam database...	0.72	0.53	1.00	9	694	0	0	0	0	8
PDB_00810	s2m links to Rfam database...	0.87	0.76	1.00	13	1068	1	0	0	1	4
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.91	0.83	1.00	20	2258	0	0	0	0	4
PDB_00876	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
PDB_01020	Purine links to Rfam database...	0.91	0.83	1.00	19	2259	1	0	0	1	4
PDB_01050	UnaL2 links to Rfam database...	0.68	0.46	1.00	6	624	2	0	0	2	7
PDB_01073	SAM links to Rfam database...	0.84	0.71	1.00	24	4347	1	0	0	1	10
PDB_01114	TPP links to Rfam database...	0.77	0.59	1.00	16	2834	1	0	0	1	11
PDB_01152	HIV_FS2 links to Rfam database...	0.80	0.64	1.00	9	552	0	0	0	0	5
PDB_01236	ykoK links to Rfam database...	0.88	0.78	1.00	42	11586	3	0	0	3	12
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00390	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00391	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00433	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00440	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00444	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1526	3	0	0	3	1
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	3	0	0	3	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	3	0	0	3	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	3	0	0	3	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	3	0	0	3	0
RFA_00589	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	4357	3	0	0	3	1
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	3	0	0	3	0
RFA_00596	Y_RNA links to Rfam database...	0.93	0.87	1.00	13	5982	3	0	0	3	2
RFA_00658	Hammerhead_1 links to Rfam database...	0.71	0.57	0.89	8	1119	2	0	1	1	6
RFA_00664	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00667	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00668	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	0.78	0.62	1.00	8	895	0	0	0	0	5
RFA_00673	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00674	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	1121	1	0	1	0	8
RFA_00675	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00677	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00680	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00704	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00707	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1029	0	0	0	0	8
RFA_00715	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	895	0	0	0	0	6
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	2	0	0	2	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00786	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00791	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5121	0	0	0	0	2
RFA_00792	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
SPR_00273	tRNA links to Rfam database...	0.44	0.24	0.83	5	2844	1	0	1	0	16
SPR_00277	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_00721	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_01157	tRNA links to Rfam database...	0.53	0.29	1.00	6	2769	0	0	0	0	15
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.96	0.92	1.00	23	2903	2	0	0	2	2
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.93	28	5535	2	1	1	0	5
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.90	0.82	1.00	27	5023	3	0	0	3	6
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.85	0.80	0.91	20	3983	6	1	1	4	5
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.85	0.81	0.90	26	6076	4	1	2	1	6
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.94	0.88	1.00	28	4725	2	0	0	2	4
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.76	0.67	0.87	20	5437	7	0	3	4	10
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.92	0.84	1.00	27	5538	3	0	0	3	5
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6302	6	1	1	4	11
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5748	2	1	1	0	6
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.68	0.66	0.70	19	6301	11	0	8	3	10
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.52	0.48	0.56	14	6530	16	0	11	5	15
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.34	0.32	0.37	11	5535	19	0	19	0	23
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.59	0.51	0.68	19	6642	11	0	9	2	18
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.65	0.65	0.67	20	5535	10	1	9	0	11
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.80	20	4070	9	1	4	4	4
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.82	0.84	0.81	21	3979	8	1	4	3	4
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.65	0.57	0.75	21	6413	9	1	6	2	16
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.89	0.79	1.00	27	5538	3	0	0	3	7
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.46	0.53	0.40	10	3630	19	3	12	4	9
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.82	0.80	0.83	20	4254	6	0	4	2	5
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	6758	4	1	1	2	10
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.73	0.69	0.77	20	4825	9	0	6	3	9
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.70	0.62	0.78	18	5972	13	0	5	8	11
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	27	6299	3	1	1	1	14
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.84	0.82	0.86	18	2829	5	0	3	2	4
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	4	0	3	1	3
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.84	0.81	0.88	21	3462	5	0	3	2	5
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	6878	7	1	1	5	12
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.83	0.76	0.90	19	4074	6	1	1	4	6
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.71	0.71	0.71	15	3219	9	0	6	3	6
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6876	6	1	2	3	12
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.75	0.74	0.77	20	4630	9	1	5	3	7
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	23	4161	6	1	1	4	2
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.86	0.84	0.88	21	3216	4	0	3	1	4
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5124	5	1	1	3	6
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	5122	3	0	2	1	6
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.88	0.81	0.96	25	5125	5	0	1	4	6
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.74	0.62	0.89	24	6876	5	1	2	2	15
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.67	0.58	0.78	21	6759	9	1	5	3	15
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6994	6	1	2	3	12
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.55	0.55	16	4627	14	2	11	1	13
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.68	0.64	0.72	21	5021	9	0	8	1	12
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	4629	5	0	2	3	6
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.89	0.88	0.91	21	3217	3	0	2	1	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.79	0.68	0.93	27	6757	3	1	1	1	13
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	27	6874	3	1	1	1	11
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	25	6876	5	1	1	3	13
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.68	0.63	0.74	20	6643	10	1	6	3	12
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	2903	5	0	4	1	4
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2902	5	0	5	0	4
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2979	5	0	5	0	4
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	4342	3	0	2	1	6
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5023	5	0	2	3	6
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.86	0.79	0.93	27	5122	3	0	2	1	7
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.90	0.81	1.00	29	5431	1	0	0	1	7
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.44	0.42	0.46	13	4725	17	0	15	2	18
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.72	0.72	0.72	18	3980	12	0	7	5	7
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.84	0.78	0.91	21	3893	4	1	1	2	6
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.80	0.73	0.88	22	5025	6	0	3	3	8
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	5328	4	1	1	2	10
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	25	6301	5	1	1	3	10
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6760	6	1	1	4	11
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	5753	7	1	1	5	12
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	22	3216	6	0	2	4	2

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Performance of Mastr(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	1741
Total TN	501582
Total FP	542
Total FP CONTRA	48
Total FP INCONS	285
Total FP COMP	209
Total FN	1604

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.680 ± 0.042
Sensitivity	0.520
Positive Predictive Value	0.839
Nr of predictions	141

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.65	0.59	0.73	24	5017	9	0	9	0	17
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00741	Entero_5_CRE links to Rfam database...	0.84	0.71	1.00	12	691	0	0	0	0	5
PDB_00810	s2m links to Rfam database...	0.51	0.41	0.64	7	1070	5	0	4	1	10
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.84	0.71	1.00	17	2261	0	0	0	0	7
PDB_00876	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
PDB_01020	Purine links to Rfam database...	0.81	0.65	1.00	15	2263	0	0	0	0	8
PDB_01050	UnaL2 links to Rfam database...	0.78	0.62	1.00	8	622	2	0	0	2	5
PDB_01073	SAM links to Rfam database...	0.34	0.24	0.50	8	4355	8	1	7	0	26
PDB_01114	TPP links to Rfam database...	0.72	0.59	0.89	16	2832	2	0	2	0	11
PDB_01152	HIV_FS2 links to Rfam database...	0.81	0.79	0.85	11	548	2	0	2	0	3
PDB_01236	ykoK links to Rfam database...	0.00	0.00	0.00	0	11628	0	0	0	0	54
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...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00396	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00402	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00409	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_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_00444	Hammerhead_3 links to Rfam database...	0.42	0.40	0.46	6	1527	10	0	7	3	9
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	14	0	0	14	0
RFA_00584	Y_RNA links to Rfam database...	0.74	0.67	0.83	10	2914	9	0	2	7	5
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	13	0	0	13	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	11	0	0	11	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	15	0	0	15	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	12	0	0	12	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	7	0	0	7	0
RFA_00594	Y_RNA links to Rfam database...	0.87	0.87	0.87	13	2760	10	0	2	8	2
RFA_00596	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	5981	19	0	0	19	1
RFA_00658	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	1117	4	0	3	1	6
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...	0.59	0.50	0.70	7	980	4	0	3	1	7
RFA_00668	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	980	4	0	3	1	7
RFA_00672	Hammerhead_1 links to Rfam database...	0.36	0.31	0.44	4	894	5	0	5	0	9
RFA_00673	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	1121	2	0	1	1	8
RFA_00674	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	1120	0	0	0	0	6
RFA_00675	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	980	4	0	3	1	7
RFA_00677	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	982	0	0	0	0	6
RFA_00678	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	939	4	0	3	1	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	1117	4	0	3	1	6
RFA_00704	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	979	4	0	3	1	6
RFA_00707	Hammerhead_1 links to Rfam database...	0.35	0.29	0.44	4	1026	5	0	5	0	10
RFA_00715	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	936	4	0	3	1	7
RFA_00717	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	891	3	0	3	0	5
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00731	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00733	s2m links to Rfam database...	0.87	0.83	0.91	10	892	3	0	1	2	2
RFA_00734	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00736	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00737	s2m links to Rfam database...	0.91	0.83	1.00	10	893	1	0	0	1	2
RFA_00745	s2m links to Rfam database...	0.91	0.83	1.00	10	936	2	0	0	2	2
RFA_00749	s2m links to Rfam database...	0.96	0.92	1.00	11	892	2	0	0	2	1
RFA_00758	s2m links to Rfam database...	0.91	0.83	1.00	10	893	2	0	0	2	2
RFA_00762	s2m links to Rfam database...	0.96	0.92	1.00	11	892	2	0	0	2	1
RFA_00763	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...	0.96	0.92	1.00	11	892	2	0	0	2	1
RFA_00786	Gammaretro_CES links to Rfam database...	0.92	0.94	0.91	30	5017	3	2	1	0	2
RFA_00791	Gammaretro_CES links to Rfam database...	0.61	0.63	0.61	20	5118	13	2	11	0	12
RFA_00792	Gammaretro_CES links to Rfam database...	0.73	0.75	0.71	24	5016	10	2	8	0	8
RFA_00801	Gammaretro_CES links to Rfam database...	0.89	0.91	0.88	29	5017	4	2	2	0	3
SPR_00273	tRNA links to Rfam database...	1.00	1.00	1.00	21	2829	0	0	0	0	0
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00721	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_01157	tRNA links to Rfam database...	0.83	0.81	0.85	17	2755	4	0	3	1	4
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.66	0.44	1.00	11	2915	0	0	0	0	14
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.94	0.94	0.94	31	5532	2	1	1	0	2
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.59	0.48	0.73	16	5028	6	0	6	0	17
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.58	0.48	0.71	12	3988	6	2	3	1	13
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.60	0.56	0.64	18	6077	12	1	9	2	14
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	4746	0	0	0	0	25
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.30	0.23	0.39	7	5442	11	0	11	0	23
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	5558	0	0	0	0	25
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	6321	0	0	0	0	28
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.75	0.59	0.95	20	5757	1	1	0	0	14
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	6321	0	0	0	0	22
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	6548	0	0	0	0	22
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5558	0	0	0	0	27
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.43	0.19	1.00	7	6663	0	0	0	0	30
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5558	7	2	5	0	31
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.71	0.56	0.90	19	5439	2	1	1	0	15
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.49	0.42	0.59	10	4078	7	1	6	0	14
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.47	0.40	0.56	10	3987	8	3	5	0	15
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.37	0.30	0.46	11	6417	14	0	13	1	26
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5558	0	0	0	0	27
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.38	0.32	0.46	6	3642	11	1	6	4	13
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4271	7	0	7	0	25
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6759	4	1	2	1	12
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	4844	0	0	0	0	22
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...	0.44	0.32	0.62	13	6307	10	1	7	2	28
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.75	0.68	0.83	15	2832	3	0	3	0	7
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.71	0.61	0.82	14	2909	3	0	3	0	9
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3479	7	7	0	0	26
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.74	0.63	0.88	22	6878	4	1	2	1	13
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.62	0.48	0.80	12	4080	4	1	2	1	13
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.46	0.29	0.75	6	3232	3	0	2	1	15
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	6896	1	0	0	1	29
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.20	0.15	0.27	4	4641	11	2	9	0	23
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.61	0.44	0.85	11	4173	2	1	1	0	14
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	7	3233	0	0	0	0	18
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.33	0.35	0.32	11	5117	24	1	22	1	20
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.65	0.47	0.89	16	5442	2	1	1	0	18
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	7	5144	0	0	0	0	26
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	7	5144	0	0	0	0	24
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.39	0.15	1.00	6	6897	1	0	0	1	33
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.82	0.78	0.88	28	6754	4	1	3	0	8
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.75	0.67	0.86	24	6993	5	1	3	1	12
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	4649	0	0	0	0	22
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.62	0.48	0.81	13	4170	3	1	2	0	14
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.83	0.70	1.00	23	5027	0	0	0	0	10
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	6	4650	1	0	0	1	25
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.43	0.29	0.64	7	3229	4	0	4	0	17
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.70	0.60	0.83	24	6757	6	1	4	1	16
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.61	0.50	0.76	19	6878	7	0	6	1	19
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.80	0.68	0.93	26	6875	4	1	1	2	12
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.66	0.56	0.78	18	6647	9	1	4	4	14
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	3	0	3	0	3
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.56	0.44	0.71	12	4169	6	1	4	1	15
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	3	0	3	0	3
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.43	0.43	0.43	10	2980	13	0	13	0	13
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.89	0.79	1.00	26	4345	0	0	0	0	7
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.57	0.32	1.00	10	5040	1	0	0	1	21
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5144	0	0	0	0	27
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	5453	0	0	0	0	29
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	7	4746	0	0	0	0	24
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	6	3999	1	0	0	1	19
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.62	0.44	0.86	12	3902	2	1	1	0	15
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.48	0.23	1.00	7	5043	0	0	0	0	23
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	5328	3	1	1	1	10
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.86	0.80	0.93	28	6298	3	1	1	1	7
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	6780	1	0	0	1	29
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5769	1	0	0	1	26
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.59	0.42	0.83	10	3228	2	0	2	0	14

^top

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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of Mastr(20) - scored lower in this pairwise comparison

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

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