CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Alterna		Mastr(seed)
MCC	0.560	>	0.309
Average MCC ± 95% Confidence Intervals	0.574 ± 0.046	>	0.206 ± 0.050
Sensitivity	0.552	>	0.118
Positive Predictive Value	0.575	<	0.815
Total TP	1632	>	349
Total TN	369911	<	372321
Total FP	1492	>	116
Total FP CONTRA	171	>	8
Total FP INCONS	1035	>	71
Total FP COMP	286	>	37
Total FN	1322	<	2605
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	1632
Total TN	369911
Total FP	1492
Total FP CONTRA	171
Total FP INCONS	1035
Total FP COMP	286
Total FN	1322

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.574 ± 0.046
Sensitivity	0.552
Positive Predictive Value	0.575
Nr of predictions	157

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00070	tRNA links to Rfam database...	0.62	0.63	0.63	15	2826	9	1	8	0	9
PDB_00392	tRNA links to Rfam database...	0.65	0.67	0.64	14	2828	8	2	6	0	7
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	21	3	18	0	23
PDB_00741	Entero_5_CRE links to Rfam database...	0.87	0.76	1.00	13	690	0	0	0	0	4
PDB_00810	s2m links to Rfam database...	0.64	0.41	1.00	7	1074	1	0	0	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...	0.77	0.71	0.85	17	2258	3	2	1	0	7
PDB_00876	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
PDB_01001	tRNA links to Rfam database...	0.52	0.56	0.50	10	2125	10	3	7	0	8
PDB_01020	Purine links to Rfam database...	0.76	0.70	0.84	16	2259	4	2	1	1	7
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01051	Telomerase-cil links to Rfam database...	0.55	0.54	0.58	7	891	6	1	4	1	6
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01114	TPP links to Rfam database...	0.56	0.48	0.65	13	2830	7	0	7	0	14
PDB_01152	HIV_FS2 links to Rfam database...	0.96	0.93	1.00	13	548	0	0	0	0	1
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
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...	0.80	0.80	0.80	12	1416	5	0	3	2	3
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00402	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	0	0	0	0	0
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	4	0	1	3	1
RFA_00425	Hammerhead_3 links to Rfam database...	0.62	0.67	0.59	10	1636	8	2	5	1	5
RFA_00427	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...	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...	0.97	0.93	1.00	14	1471	2	0	0	2	1
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...	0.97	0.93	1.00	14	1526	1	0	0	1	1
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00583	Y_RNA links to Rfam database...	0.93	0.93	0.93	14	4935	17	0	1	16	1
RFA_00584	Y_RNA links to Rfam database...	0.87	0.87	0.87	13	2911	16	0	2	14	2
RFA_00585	Y_RNA links to Rfam database...	0.93	0.93	0.93	14	4836	15	0	1	14	1
RFA_00586	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	3902	8	0	0	8	1
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	14	0	0	14	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	13	0	0	13	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	19	0	0	19	0
RFA_00594	Y_RNA links to Rfam database...	0.90	0.87	0.93	13	2761	12	0	1	11	2
RFA_00632	HDV_ribozyme links to Rfam database...	0.24	0.25	0.23	7	4065	23	3	20	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.50	0.46	0.54	13	3981	13	3	8	2	15
RFA_00642	Vimentin3 links to Rfam database...	0.16	0.17	0.17	3	2908	15	0	15	0	15
RFA_00643	Vimentin3 links to Rfam database...	0.24	0.22	0.27	4	2196	12	2	9	1	14
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2682	19	3	16	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2397	18	5	13	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.31	0.33	0.30	6	2125	14	0	14	0	12
RFA_00651	Vimentin3 links to Rfam database...	0.35	0.33	0.38	6	2064	10	1	9	0	12
RFA_00653	Vimentin3 links to Rfam database...	0.34	0.33	0.35	6	2128	14	2	9	3	12
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2399	16	2	14	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	5	0	3	2	5
RFA_00659	Hammerhead_1 links to Rfam database...	0.30	0.29	0.33	4	1116	10	0	8	2	10
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	10	0	10	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.29	0.29	0.31	4	977	10	1	8	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	983	1	0	1	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	895	9	0	8	1	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	1118	6	0	5	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	4	0	3	1	4
RFA_00675	Hammerhead_1 links to Rfam database...	0.29	0.29	0.31	4	977	9	1	8	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.59	0.57	0.62	8	977	7	0	5	2	6
RFA_00678	Hammerhead_1 links to Rfam database...	0.80	0.64	1.00	9	937	0	0	0	0	5
RFA_00680	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	6	0	3	3	4
RFA_00684	Hammerhead_1 links to Rfam database...	0.77	0.71	0.83	10	978	4	0	2	2	4
RFA_00685	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00703	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	4266	16	1	2	13	5
RFA_00704	Hammerhead_1 links to Rfam database...	0.36	0.36	0.38	5	977	9	0	8	1	9
RFA_00705	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1022	4	0	3	1	4
RFA_00706	Hammerhead_1 links to Rfam database...	0.31	0.29	0.36	4	1024	7	0	7	0	10
RFA_00707	Hammerhead_1 links to Rfam database...	0.31	0.29	0.36	4	1024	7	0	7	0	10
RFA_00708	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1025	4	0	3	1	7
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	982	9	0	8	1	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.38	0.36	0.42	5	978	8	0	7	1	9
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	0	9	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	933	13	0	13	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	936	10	0	10	0	14
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...	0.69	0.67	0.73	8	892	5	1	2	2	4
RFA_00731	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00733	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00736	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00737	s2m links to Rfam database...	0.39	0.42	0.38	5	890	9	2	6	1	7
RFA_00745	s2m links to Rfam database...	0.43	0.42	0.45	5	935	7	1	5	1	7
RFA_00749	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00758	s2m links to Rfam database...	0.57	0.33	1.00	4	899	1	0	0	1	8
RFA_00762	s2m links to Rfam database...	0.64	0.67	0.62	8	890	6	1	4	1	4
RFA_00763	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00764	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00765	s2m links to Rfam database...	0.81	0.67	1.00	8	895	2	0	0	2	4
RFA_00767	Corona_pk3 links to Rfam database...	0.54	0.50	0.60	9	1876	6	2	4	0	9
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	9	0	6	3	10
RFA_00769	Corona_pk3 links to Rfam database...	0.38	0.39	0.39	7	1935	11	2	9	0	11
RFA_00770	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	2003	9	0	6	3	11
RFA_00773	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	1940	9	0	6	3	11
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	1999	19	3	14	2	16
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	11	0	9	2	10
SPR_00020	tRNA links to Rfam database...	0.79	0.75	0.83	15	2683	6	0	3	3	5
SPR_00023	tRNA links to Rfam database...	0.47	0.52	0.42	11	2824	15	5	10	0	10
SPR_00064	tRNA links to Rfam database...	0.54	0.57	0.52	12	2827	11	2	9	0	9
SPR_00111	tRNA links to Rfam database...	0.54	0.57	0.52	12	2678	11	1	10	0	9
SPR_00113	tRNA links to Rfam database...	0.77	0.75	0.79	15	2756	7	0	4	3	5
SPR_00137	tRNA links to Rfam database...	0.84	0.86	0.82	18	2904	10	0	4	6	3
SPR_00273	tRNA links to Rfam database...	0.23	0.24	0.24	5	2829	17	0	16	1	16
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00279	tRNA links to Rfam database...	0.36	0.33	0.39	7	2908	11	6	5	0	14
SPR_00314	tRNA links to Rfam database...	0.74	0.81	0.68	17	2901	11	0	8	3	4
SPR_00394	tRNA links to Rfam database...	0.57	0.57	0.57	12	3634	14	5	4	5	9
SPR_00402	tRNA links to Rfam database...	0.62	0.62	0.62	13	2535	8	1	7	0	8
SPR_00434	tRNA links to Rfam database...	0.32	0.33	0.32	7	2828	15	3	12	0	14
SPR_00452	tRNA links to Rfam database...	0.73	0.76	0.70	16	2827	7	3	4	0	5
SPR_00595	tRNA links to Rfam database...	0.78	0.76	0.80	16	2755	4	2	2	0	5
SPR_00721	tRNA links to Rfam database...	0.52	0.57	0.48	12	2901	15	1	12	2	9
SPR_00816	tRNA links to Rfam database...	0.32	0.35	0.29	7	3462	20	5	12	3	13
SPR_00867	tRNA links to Rfam database...	0.48	0.52	0.44	11	2901	16	4	10	2	10
SPR_00912	tRNA links to Rfam database...	0.49	0.52	0.46	11	2979	16	3	10	3	10
SPR_01157	tRNA links to Rfam database...	0.73	0.76	0.70	16	2752	8	0	7	1	5
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.66	0.68	0.65	17	2900	11	0	9	2	8
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.50	0.48	0.52	12	3982	12	2	9	1	13
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.56	0.56	0.56	18	4721	15	1	13	1	14
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.68	0.71	0.65	17	4069	10	1	8	1	7
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.25	0.28	0.24	7	3976	22	2	20	0	18
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.12	0.16	0.10	3	3625	29	6	21	2	16
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.45	0.48	0.43	12	4250	16	4	12	0	13
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.66	0.69	0.65	20	4820	14	0	11	3	9
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.36	0.40	0.33	10	4156	22	3	17	2	15
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.44	0.45	0.43	10	2827	13	3	10	0	12
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.58	0.61	0.56	14	2901	13	2	9	2	9
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.45	0.46	0.44	12	3459	16	4	11	1	14
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.34	0.36	0.33	9	4068	19	0	18	1	16
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.73	0.76	0.70	16	3217	10	0	7	3	5
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.35	0.37	0.33	10	4626	20	3	17	0	17
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.37	0.40	0.36	10	4158	18	1	17	0	15
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.41	0.40	0.43	10	3217	14	1	12	1	15
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.85	0.85	0.85	23	3376	5	1	3	1	4
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.87	0.83	0.91	20	3299	3	0	2	1	4
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.89	0.87	0.91	20	3299	3	0	2	1	3
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.84	0.84	0.84	21	3056	5	1	3	1	4
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.32	0.34	0.30	10	4623	23	4	19	0	19
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.48	0.48	0.48	13	4159	15	1	13	1	14
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.43	0.45	0.41	14	4622	20	2	18	0	17
SRP_00271	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3215	25	3	22	0	24
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.77	0.73	0.81	22	3714	6	0	5	1	8
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.40	0.43	0.38	10	2900	16	1	15	0	13
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.35	0.37	0.34	10	4157	19	0	19	0	17
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	2903	5	0	4	1	4
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	2980	5	0	4	1	4
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.73	0.73	0.73	24	4338	9	1	8	0	9
SRP_00341	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4726	27	5	22	0	31
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.57	0.60	0.56	15	3978	17	1	11	5	10
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.36	0.33	0.39	9	3893	14	2	12	0	18
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.92	0.93	0.90	28	4722	6	0	3	3	2
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.39	0.37	0.42	10	3379	15	2	12	1	17
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.12	0.13	0.13	3	3216	21	4	17	0	21

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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	349
Total TN	372321
Total FP	116
Total FP CONTRA	8
Total FP INCONS	71
Total FP COMP	37
Total FN	2605

Total Scores
MCC	0.309
Average MCC ± 95% Confidence Intervals	0.206 ± 0.050
Sensitivity	0.118
Positive Predictive Value	0.815
Nr of predictions	157

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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
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.60	0.43	0.86	6	939	2	0	1	1	8
PDB_00012	mir-TAR links to Rfam database...	0.00	0.00	0.00	0	406	0	0	0	0	7
PDB_00070	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	24
PDB_00392	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
PDB_00553	mir-TAR links to Rfam database...	0.00	0.00	0.00	0	465	0	0	0	0	11
PDB_00716	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	23
PDB_00741	Entero_5_CRE links to Rfam database...	0.00	0.00	0.00	0	703	0	0	0	0	17
PDB_00810	s2m links to Rfam database...	0.43	0.35	0.55	6	1070	6	0	5	1	11
PDB_00828	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	27
PDB_00829	Purine links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	24
PDB_00876	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	20
PDB_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
PDB_01020	Purine links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	23
PDB_01050	UnaL2 links to Rfam database...	0.78	0.62	1.00	8	622	2	0	0	2	5
PDB_01051	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
PDB_01073	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	34
PDB_01114	TPP links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	27
PDB_01152	HIV_FS2 links to Rfam database...	0.81	0.79	0.85	11	548	2	0	2	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00391	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00396	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00402	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00409	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_00425	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1653	0	0	0	0	15
RFA_00427	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_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_00440	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	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_00444	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1540	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_00449	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00583	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4950	0	0	0	0	15
RFA_00584	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	15
RFA_00585	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4851	0	0	0	0	15
RFA_00586	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	3916	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_00588	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4560	0	0	0	0	15
RFA_00589	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	15
RFA_00594	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	15
RFA_00632	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	28
RFA_00636	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	28
RFA_00642	Vimentin3 links to Rfam database...	0.58	0.33	1.00	6	2920	0	0	0	0	12
RFA_00643	Vimentin3 links to Rfam database...	0.29	0.17	0.50	3	2205	3	0	3	0	15
RFA_00644	Vimentin3 links to Rfam database...	0.62	0.39	1.00	7	2694	0	0	0	0	11
RFA_00645	Vimentin3 links to Rfam database...	0.58	0.33	1.00	6	2409	0	0	0	0	12
RFA_00649	Vimentin3 links to Rfam database...	0.67	0.44	1.00	8	2137	0	0	0	0	10
RFA_00651	Vimentin3 links to Rfam database...	0.67	0.44	1.00	8	2072	0	0	0	0	10
RFA_00653	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2143	2	0	2	0	18
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_00659	Hammerhead_1 links to Rfam database...	0.50	0.36	0.71	5	1121	3	0	2	1	9
RFA_00664	Hammerhead_1 links to Rfam database...	0.27	0.07	1.00	1	989	0	0	0	0	13
RFA_00667	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	988	2	0	2	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.50	0.36	0.71	5	983	3	0	2	1	9
RFA_00672	Hammerhead_1 links to Rfam database...	0.28	0.08	1.00	1	902	0	0	0	0	12
RFA_00673	Hammerhead_1 links to Rfam database...	0.46	0.21	1.00	3	1125	0	0	0	0	11
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_00678	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	2	0	2	0	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00684	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00685	Hammerhead_1 links to Rfam database...	0.56	0.43	0.75	6	982	3	0	2	1	8
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4270	8	3	5	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	988	2	0	2	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.27	0.07	1.00	1	1034	0	0	0	0	13
RFA_00706	Hammerhead_1 links to Rfam database...	0.30	0.14	0.67	2	1032	1	0	1	0	12
RFA_00707	Hammerhead_1 links to Rfam database...	0.50	0.36	0.71	5	1028	3	0	2	1	9
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.21	0.75	3	1031	1	0	1	0	11
RFA_00709	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00710	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00711	Hammerhead_1 links to Rfam database...	0.27	0.07	1.00	1	1034	0	0	0	0	13
RFA_00715	Hammerhead_1 links to Rfam database...	0.35	0.21	0.60	3	941	2	0	2	0	11
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_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...	0.91	0.83	1.00	10	893	2	0	0	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	2	0	0	2	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...	0.91	0.83	1.00	10	893	2	0	0	2	2
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...	0.91	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_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
SPR_00020	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	20
SPR_00023	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
SPR_00064	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
SPR_00111	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	21
SPR_00113	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	20
SPR_00137	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00273	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
SPR_00277	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00279	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00314	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00394	tRNA links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	21
SPR_00402	tRNA links to Rfam database...	0.00	0.00	0.00	0	2556	0	0	0	0	21
SPR_00434	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	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
SPR_00595	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	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
SPR_00816	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	20
SPR_00867	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00912	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	21
SPR_01157	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	21
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	25
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	25
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	32
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	24
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	25
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	19
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4278	0	0	0	0	25
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4851	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_00161	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	22
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	26
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_00209	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4656	0	0	0	0	27
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	25
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3240	0	0	0	0	25
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3403	0	0	0	0	27
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3321	0	0	0	0	24
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3321	0	0	0	0	23
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3081	0	0	0	0	25
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4656	0	0	0	0	29
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	27
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4656	0	0	0	0	31
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3240	0	0	0	0	24
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	27
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	23
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	33
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	25
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	27
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	30
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3403	0	0	0	0	27
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3240	0	0	0	0	24

^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 Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

2. Individual counts for Alterna [ 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 ]