CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		ProbKnot
MCC	0.750	>	0.684
Average MCC ± 95% Confidence Intervals	0.757 ± 0.026	>	0.667 ± 0.038
Sensitivity	0.712	>	0.678
Positive Predictive Value	0.793	>	0.694
Total TP	3967	>	3780
Total TN	929654	>	929207
Total FP	1620	<	2217
Total FP CONTRA	135	<	264
Total FP INCONS	899	<	1404
Total FP COMP	586	>	549
Total FN	1605	<	1792
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and ProbKnot. 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 MXScarna(seed) and ProbKnot).
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 MXScarna(seed) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and ProbKnot. 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 MXScarna(seed) and ProbKnot).

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

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

Total Base Pair Counts
Total TP	3967
Total TN	929654
Total FP	1620
Total FP CONTRA	135
Total FP INCONS	899
Total FP COMP	586
Total FN	1605

Total Scores
MCC	0.750
Average MCC ± 95% Confidence Intervals	0.757 ± 0.026
Sensitivity	0.712
Positive Predictive Value	0.793
Nr of predictions	233

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00251	RNaseP_nuc links to Rfam database...	0.00	0.00	0.00	0	17757	12	1	8	3	43
CRW_01484	5S_rRNA links to Rfam database...	0.75	0.69	0.82	27	7470	10	0	6	4	12
CRW_01499	5S_rRNA links to Rfam database...	0.66	0.61	0.71	25	7966	12	0	10	2	16
CRW_01507	5S_rRNA links to Rfam database...	0.78	0.73	0.83	30	7467	9	0	6	3	11
CRW_01535	5S_rRNA links to Rfam database...	0.89	0.89	0.89	33	7103	8	0	4	4	4
CRW_01590	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	7103	7	0	3	4	3
CRW_01603	5S_rRNA links to Rfam database...	0.89	0.89	0.89	33	7103	8	0	4	4	4
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.59	0.36	1.00	5	941	0	0	0	0	9
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...	0.81	0.73	0.91	30	5017	3	0	3	0	11
PDB_00392	tRNA links to Rfam database...	0.90	0.90	0.90	19	2829	2	0	2	0	2
PDB_00553	mir-TAR links to Rfam database...	0.90	0.82	1.00	9	456	0	0	0	0	2
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2681	21	1	19	1	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...	0.77	0.65	0.92	11	1069	2	0	1	1	6
PDB_00828	Purine links to Rfam database...	0.82	0.67	1.00	18	2467	0	0	0	0	9
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00876	HIV_FE links to Rfam database...	0.57	0.55	0.61	11	972	7	0	7	0	9
PDB_01001	tRNA links to Rfam database...	0.61	0.56	0.67	10	2130	6	3	2	1	8
PDB_01020	Purine links to Rfam database...	0.83	0.70	1.00	16	2262	0	0	0	0	7
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...	0.64	0.54	0.78	7	894	5	0	2	3	6
PDB_01073	SAM links to Rfam database...	0.81	0.74	0.89	25	4343	4	1	2	1	9
PDB_01092	glmS links to Rfam database...	0.70	0.63	0.79	33	10111	12	2	7	3	19
PDB_01114	TPP links to Rfam database...	0.53	0.48	0.59	13	2828	11	0	9	2	14
PDB_01152	HIV_FS2 links to Rfam database...	0.85	0.79	0.92	11	549	1	0	1	0	3
PDB_01236	ykoK links to Rfam database...	0.87	0.81	0.94	44	11581	8	0	3	5	10
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00390	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00391	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00425	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1640	1	0	0	1	2
RFA_00427	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00440	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00444	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1526	2	0	0	2	1
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00582	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	5980	19	0	0	19	0
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	19	0	0	19	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	11	0	0	11	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	19	0	0	19	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	16	0	0	16	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	19	0	0	19	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	15	0	0	15	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	17	0	0	17	0
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	11	0	0	11	0
RFA_00596	Y_RNA links to Rfam database...	0.93	0.87	1.00	13	5982	19	0	0	19	2
RFA_00603	Telomerase-cil links to Rfam database...	0.74	0.74	0.74	26	13495	17	3	6	8	9
RFA_00604	Telomerase-cil links to Rfam database...	0.72	0.63	0.81	22	13503	13	3	2	8	13
RFA_00605	Telomerase-cil links to Rfam database...	0.26	0.23	0.30	8	15198	22	5	14	3	27
RFA_00607	Telomerase-cil links to Rfam database...	0.77	0.72	0.81	26	17734	16	1	5	10	10
RFA_00609	Telomerase-cil links to Rfam database...	0.67	0.65	0.69	24	17920	19	2	9	8	13
RFA_00610	Telomerase-cil links to Rfam database...	0.76	0.76	0.76	28	17168	19	1	8	10	9
RFA_00611	Telomerase-cil links to Rfam database...	0.75	0.74	0.76	26	13007	13	4	4	5	9
RFA_00613	Telomerase-cil links to Rfam database...	0.76	0.71	0.81	25	12849	11	4	2	5	10
RFA_00615	Telomerase-cil links to Rfam database...	0.75	0.74	0.76	26	13332	15	4	4	7	9
RFA_00632	HDV_ribozyme links to Rfam database...	0.25	0.25	0.27	7	4069	19	1	18	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.35	0.36	0.36	10	3977	18	2	16	0	18
RFA_00642	Vimentin3 links to Rfam database...	0.56	0.50	0.64	9	2912	7	0	5	2	9
RFA_00643	Vimentin3 links to Rfam database...	0.69	0.61	0.79	11	2197	5	0	3	2	7
RFA_00644	Vimentin3 links to Rfam database...	0.69	0.61	0.79	11	2687	5	0	3	2	7
RFA_00645	Vimentin3 links to Rfam database...	0.30	0.28	0.33	5	2400	11	0	10	1	13
RFA_00649	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2130	5	0	3	2	6
RFA_00651	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2065	5	0	3	2	6
RFA_00653	Vimentin3 links to Rfam database...	0.67	0.61	0.73	11	2130	6	0	4	2	7
RFA_00654	Vimentin3 links to Rfam database...	0.73	0.67	0.80	12	2400	5	0	3	2	6
RFA_00658	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
RFA_00659	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	1116	7	0	6	1	8
RFA_00664	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00667	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00668	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00672	Hammerhead_1 links to Rfam database...	0.72	0.69	0.75	9	891	4	0	3	1	4
RFA_00673	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
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...	0.69	0.64	0.75	9	978	4	0	3	1	5
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...	0.66	0.64	0.69	9	933	5	0	4	1	5
RFA_00680	Hammerhead_1 links to Rfam database...	0.61	0.57	0.67	8	1116	5	0	4	1	6
RFA_00684	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	977	5	0	4	1	5
RFA_00685	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00695	Hammerhead_1 links to Rfam database...	0.62	0.57	0.67	8	7009	22	1	3	18	6
RFA_00703	Hammerhead_1 links to Rfam database...	0.62	0.57	0.67	8	4266	8	1	3	4	6
RFA_00704	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00705	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	1022	5	0	4	1	5
RFA_00706	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00707	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00708	Hammerhead_1 links to Rfam database...	0.64	0.57	0.73	8	1024	4	0	3	1	6
RFA_00709	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00710	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00711	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1023	4	0	3	1	5
RFA_00715	Hammerhead_1 links to Rfam database...	0.56	0.50	0.64	7	935	5	0	4	1	7
RFA_00716	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	935	6	0	5	1	8
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...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	1	0	0	1	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00763	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...	0.59	0.56	0.63	10	1875	6	2	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	2	4	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...	0.57	0.56	0.59	10	1999	7	2	5	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.57	0.56	0.59	10	1936	7	2	5	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.92	0.91	0.94	29	5019	3	2	0	1	3
RFA_00786	Gammaretro_CES links to Rfam database...	0.92	0.91	0.94	29	5019	3	2	0	1	3
RFA_00791	Gammaretro_CES links to Rfam database...	0.87	0.88	0.88	28	5119	5	2	2	1	4
RFA_00792	Gammaretro_CES links to Rfam database...	0.92	0.91	0.94	29	5019	3	2	0	1	3
RFA_00801	Gammaretro_CES links to Rfam database...	0.91	0.91	0.91	29	5018	4	2	1	1	3
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	19	2	14	3	16
RFA_00809	RydC links to Rfam database...	0.30	0.31	0.29	5	2128	12	1	11	0	11
SPR_00020	tRNA links to Rfam database...	0.97	0.95	1.00	19	2682	1	0	0	1	1
SPR_00023	tRNA links to Rfam database...	0.77	0.71	0.83	15	2832	4	0	3	1	6
SPR_00064	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00111	tRNA links to Rfam database...	0.98	0.95	1.00	20	2681	0	0	0	0	1
SPR_00113	tRNA links to Rfam database...	0.31	0.25	0.38	5	2762	9	0	8	1	15
SPR_00137	tRNA links to Rfam database...	0.82	0.76	0.89	16	2908	4	0	2	2	5
SPR_00273	tRNA links to Rfam database...	0.58	0.57	0.60	12	2830	8	0	8	0	9
SPR_00277	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00279	tRNA links to Rfam database...	0.95	0.90	1.00	19	2907	1	0	0	1	2
SPR_00314	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00394	tRNA links to Rfam database...	0.73	0.71	0.75	15	3635	5	0	5	0	6
SPR_00402	tRNA links to Rfam database...	0.98	0.95	1.00	20	2536	0	0	0	0	1
SPR_00434	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00452	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00595	tRNA links to Rfam database...	0.98	0.95	1.00	20	2755	0	0	0	0	1
SPR_00721	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00816	tRNA links to Rfam database...	0.52	0.50	0.56	10	3468	9	0	8	1	10
SPR_00867	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00912	tRNA links to Rfam database...	1.00	1.00	1.00	21	2982	0	0	0	0	0
SPR_01157	tRNA links to Rfam database...	0.98	0.95	1.00	20	2755	0	0	0	0	1
SRP_00001	Bacteria_large_SRP links to Rfam database...	0.77	0.70	0.85	28	6753	6	1	4	1	12
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.55	0.52	0.59	13	2904	10	0	9	1	12
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	30	5531	5	1	3	1	3
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.73	0.70	0.77	23	5020	9	0	7	2	10
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.53	0.52	0.55	16	5536	16	1	12	3	15
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.54	0.52	0.57	13	3982	13	1	9	3	12
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.44	0.41	0.48	12	5025	14	2	11	1	17
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.82	0.81	0.84	26	6074	9	1	4	4	6
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.95	0.94	0.97	30	4722	3	0	1	2	2
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.76	0.73	0.79	22	5432	10	0	6	4	8
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.76	0.75	0.77	24	5534	9	0	7	2	8
SRP_00056	Bacteria_small_SRP links to Rfam database...	0.73	0.65	0.83	24	6412	8	1	4	3	13
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.72	0.66	0.79	23	6299	10	1	5	4	12
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.83	0.82	0.85	28	5745	7	1	4	2	6
SRP_00067	Bacteria_small_SRP links to Rfam database...	0.80	0.71	0.90	27	5748	5	1	2	2	11
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.46	0.41	0.52	12	6305	13	0	11	2	17
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.42	0.41	0.43	12	6527	21	2	14	5	17
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.86	0.82	0.90	28	5534	5	0	3	2	6
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.69	0.62	0.77	23	6640	10	0	7	3	14
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.51	0.52	0.50	16	5533	17	2	14	1	15
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	32	5425	3	1	2	0	2
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.62	0.58	0.67	14	4074	12	1	6	5	10
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.65	0.60	0.71	15	3984	10	1	5	4	10
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.80	0.73	0.87	27	6410	6	1	3	2	10
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.80	0.74	0.86	25	5536	8	0	4	4	9
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.67	0.72	0.62	18	5224	14	4	7	3	7
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.26	0.26	0.26	5	3636	16	2	12	2	14
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.60	0.64	0.57	16	4250	13	4	8	1	9
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.82	0.78	0.88	28	6754	7	1	3	3	8
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.63	0.62	0.64	18	4823	14	0	10	4	11
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.65	0.69	0.63	20	5963	14	2	10	2	9
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.60	0.64	0.57	16	4158	13	3	9	1	9
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.81	0.73	0.91	30	6295	5	1	2	2	11
SRP_00145	Bacteria_small_SRP links to Rfam database...	0.74	0.68	0.82	27	6295	8	1	5	2	13
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.82	0.75	0.90	27	5223	5	1	2	2	9
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.84	0.86	0.83	19	2827	6	0	4	2	3
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	21	2902	5	0	3	2	2
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.85	23	3459	6	0	4	2	3
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.75	0.66	0.85	23	6876	7	1	3	3	12
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.51	0.48	0.55	12	4073	14	1	9	4	13
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.74	0.76	0.73	16	3218	9	0	6	3	5
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.72	0.67	0.77	24	6872	10	1	6	3	12
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.43	0.41	0.46	11	4632	15	1	12	2	16
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.66	0.56	0.78	14	4168	9	1	3	5	11
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.88	0.88	0.88	22	3215	4	0	3	1	3
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.76	0.70	0.83	19	3380	6	1	3	2	8
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.74	0.71	0.77	17	3299	7	0	5	2	7
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	3298	7	0	4	3	4
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.83	0.76	0.90	19	3060	4	1	1	2	6
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.81	0.81	0.81	25	5120	7	1	5	1	6
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.40	0.41	0.41	11	5226	20	0	16	4	16
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
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...	0.78	0.74	0.82	23	5123	6	0	5	1	8
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.71	0.64	0.78	25	6871	10	1	6	3	14
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.76	0.72	0.81	26	6754	9	1	5	3	10
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.76	0.72	0.81	26	6989	9	2	4	3	10
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.57	0.59	0.57	17	4626	14	2	11	1	12
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.57	0.56	0.60	15	4161	12	1	9	2	12
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	5021	3	0	2	1	6
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.93	0.87	1.00	27	4629	4	0	0	4	4
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.57	0.50	0.67	12	3222	6	0	6	0	12
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.74	0.65	0.84	26	6755	8	1	4	3	14
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.79	0.71	0.87	27	6872	7	1	3	3	11
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.86	0.80	0.92	24	3715	3	0	2	1	6
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.80	0.71	0.90	27	6873	8	1	2	5	11
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.71	0.69	0.73	22	6640	13	1	7	5	10
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.76	0.78	0.75	18	2902	7	0	6	1	5
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.44	0.41	0.48	11	4163	15	1	11	3	16
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.75	0.78	0.72	18	2901	7	0	7	0	5
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.71	0.70	0.73	16	2981	6	0	6	0	7
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.47	0.48	0.47	14	5326	16	3	13	0	15
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.92	0.85	1.00	28	4343	2	0	0	2	5
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.90	0.84	0.96	26	5023	4	0	1	3	5
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.92	0.88	0.97	30	5120	2	0	1	1	4
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.75	0.72	0.79	26	5427	8	0	7	1	10
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.46	0.45	0.47	14	4723	16	0	16	0	17
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.71	0.68	0.74	17	3982	8	1	5	2	8
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.37	0.33	0.43	9	3895	14	1	11	2	18
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.57	0.50	0.65	15	5027	11	0	8	3	15
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.85	0.81	0.91	29	5324	5	1	2	2	7
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.83	0.77	0.90	27	6298	6	1	2	3	8
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.91	0.90	0.93	27	4724	6	0	2	4	3
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.82	0.74	0.91	20	3381	4	0	2	2	7
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.72	0.66	0.79	23	6757	11	1	5	5	12
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.75	0.69	0.83	24	5749	11	1	4	6	11
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.75	0.67	0.84	16	3221	5	0	3	2	8

^top

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	3780
Total TN	929207
Total FP	2217
Total FP CONTRA	264
Total FP INCONS	1404
Total FP COMP	549
Total FN	1792

Total Scores
MCC	0.684
Average MCC ± 95% Confidence Intervals	0.667 ± 0.038
Sensitivity	0.678
Positive Predictive Value	0.694
Nr of predictions	233

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00251	RNaseP_nuc links to Rfam database...	1.00	1.00	1.00	43	17723	24	0	0	24	0
CRW_01484	5S_rRNA links to Rfam database...	0.25	0.26	0.26	10	7464	31	4	25	2	29
CRW_01499	5S_rRNA links to Rfam database...	0.33	0.34	0.33	14	7959	30	2	26	2	27
CRW_01507	5S_rRNA links to Rfam database...	0.86	0.76	0.97	31	7471	4	0	1	3	10
CRW_01535	5S_rRNA links to Rfam database...	0.91	0.84	1.00	31	7109	2	0	0	2	6
CRW_01590	5S_rRNA links to Rfam database...	0.23	0.24	0.23	9	7101	30	4	26	0	28
CRW_01603	5S_rRNA links to Rfam database...	0.81	0.76	0.88	28	7108	6	0	4	2	9
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.78	0.79	0.79	11	932	3	0	3	0	3
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	4	0	0	4	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.94	0.88	1.00	36	5014	0	0	0	0	5
PDB_00392	tRNA links to Rfam database...	0.61	0.67	0.56	14	2825	11	5	6	0	7
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	1	0	0	1	0
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	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...	0.76	0.59	1.00	10	1071	0	0	0	0	7
PDB_00828	Purine links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
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...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01050	UnaL2 links to Rfam database...	0.88	0.85	0.92	11	618	3	0	1	2	2
PDB_01051	Telomerase-cil links to Rfam database...	0.88	0.85	0.92	11	891	5	0	1	4	2
PDB_01073	SAM links to Rfam database...	0.86	0.74	1.00	25	4346	1	0	0	1	9
PDB_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01114	TPP links to Rfam database...	0.50	0.41	0.61	11	2832	7	0	7	0	16
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
PDB_01236	ykoK links to Rfam database...	0.74	0.70	0.78	38	11579	14	0	11	3	16
RFA_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
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...	0.93	0.87	1.00	13	1418	2	0	0	2	2
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...	0.33	0.33	0.33	5	1416	11	0	10	1	10
RFA_00409	Hammerhead_3 links to Rfam database...	0.67	0.60	0.75	9	1419	5	1	2	2	6
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00425	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1640	4	0	0	4	2
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	3	0	0	3	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	3	0	0	3	0
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00444	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1525	2	0	0	2	0
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_00582	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	5980	21	0	0	21	0
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...	0.87	0.87	0.87	13	2911	14	0	2	12	2
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	14	0	0	14	0
RFA_00586	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	3902	16	0	0	16	1
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	12	0	0	12	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	16	0	0	16	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	15	0	0	15	0
RFA_00594	Y_RNA links to Rfam database...	0.90	0.87	0.93	13	2761	10	0	1	9	2
RFA_00596	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	5976	32	5	14	13	15
RFA_00603	Telomerase-cil links to Rfam database...	0.67	0.74	0.60	26	13487	22	4	13	5	9
RFA_00604	Telomerase-cil links to Rfam database...	0.71	0.74	0.68	26	13492	23	2	10	11	9
RFA_00605	Telomerase-cil links to Rfam database...	0.30	0.34	0.27	12	15180	46	3	30	13	23
RFA_00607	Telomerase-cil links to Rfam database...	0.83	0.83	0.83	30	17730	17	4	2	11	6
RFA_00609	Telomerase-cil links to Rfam database...	0.53	0.59	0.47	22	17908	35	6	19	10	15
RFA_00610	Telomerase-cil links to Rfam database...	0.88	0.86	0.89	32	17169	12	0	4	8	5
RFA_00611	Telomerase-cil links to Rfam database...	0.80	0.80	0.80	28	13006	18	3	4	11	7
RFA_00613	Telomerase-cil links to Rfam database...	0.71	0.69	0.73	24	12847	17	4	5	8	11
RFA_00615	Telomerase-cil links to Rfam database...	0.62	0.69	0.56	24	13323	21	8	11	2	11
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	4068	16	0	16	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.44	0.46	0.43	13	3975	17	0	17	0	15
RFA_00642	Vimentin3 links to Rfam database...	0.39	0.33	0.46	6	2913	7	2	5	0	12
RFA_00643	Vimentin3 links to Rfam database...	0.30	0.28	0.33	5	2196	11	2	8	1	13
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2685	16	5	11	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2404	11	2	9	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.75	0.78	0.74	14	2126	8	1	4	3	4
RFA_00651	Vimentin3 links to Rfam database...	0.25	0.22	0.29	4	2066	12	0	10	2	14
RFA_00653	Vimentin3 links to Rfam database...	0.34	0.33	0.35	6	2128	11	2	9	0	12
RFA_00654	Vimentin3 links to Rfam database...	0.23	0.22	0.25	4	2399	12	2	10	0	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1122	8	0	6	2	14
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.30	0.29	0.33	4	978	8	1	7	0	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.41	0.43	0.40	6	975	9	0	9	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...	0.44	0.36	0.56	5	1119	5	0	4	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	1118	5	0	5	0	9
RFA_00675	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	978	7	0	6	1	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.37	0.29	0.50	4	938	4	0	4	0	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	7	0	3	4	4
RFA_00684	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	977	6	0	4	2	5
RFA_00685	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00695	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	7007	24	1	4	19	5
RFA_00703	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	4264	17	1	4	12	5
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	988	3	0	2	1	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.69	0.71	0.67	10	1020	5	0	5	0	4
RFA_00706	Hammerhead_1 links to Rfam database...	0.25	0.21	0.30	3	1025	7	0	7	0	11
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1027	8	0	8	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	1025	6	0	6	0	10
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	982	8	0	8	0	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.07	0.07	0.10	1	980	9	0	9	0	13
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1023	12	0	12	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...	0.64	0.64	0.64	9	889	5	0	5	0	5
RFA_00730	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00731	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00733	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00734	s2m links to Rfam database...	0.73	0.67	0.80	8	893	3	0	2	1	4
RFA_00736	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00737	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00745	s2m links to Rfam database...	0.81	0.67	1.00	8	938	1	0	0	1	4
RFA_00749	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00758	s2m links to Rfam database...	0.76	0.58	1.00	7	896	0	0	0	0	5
RFA_00762	s2m links to Rfam database...	0.64	0.67	0.62	8	890	5	1	4	0	4
RFA_00763	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00764	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00765	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.44	0.44	0.44	8	1873	11	1	9	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	2000	9	0	6	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.73	0.75	0.71	24	5016	11	2	8	1	8
RFA_00786	Gammaretro_CES links to Rfam database...	0.64	0.66	0.64	21	5017	12	2	10	0	11
RFA_00791	Gammaretro_CES links to Rfam database...	0.86	0.84	0.87	27	5120	6	2	2	2	5
RFA_00792	Gammaretro_CES links to Rfam database...	0.95	0.94	0.97	30	5019	3	0	1	2	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.76	0.78	0.74	25	5016	11	2	7	2	7
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	0	3	0	7
RFA_00809	RydC links to Rfam database...	0.35	0.38	0.33	6	2127	12	1	11	0	10
SPR_00020	tRNA links to Rfam database...	0.76	0.80	0.73	16	2679	9	2	4	3	4
SPR_00023	tRNA links to Rfam database...	0.50	0.52	0.48	11	2827	12	3	9	0	10
SPR_00064	tRNA links to Rfam database...	0.58	0.57	0.60	12	2830	8	2	6	0	9
SPR_00111	tRNA links to Rfam database...	1.00	1.00	1.00	21	2680	1	0	0	1	0
SPR_00113	tRNA links to Rfam database...	1.00	1.00	1.00	20	2755	6	0	0	6	0
SPR_00137	tRNA links to Rfam database...	0.77	0.86	0.69	18	2900	14	4	4	6	3
SPR_00273	tRNA links to Rfam database...	0.29	0.33	0.27	7	2824	20	2	17	1	14
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	1	0	0	1	0
SPR_00279	tRNA links to Rfam database...	0.47	0.48	0.48	10	2905	11	6	5	0	11
SPR_00314	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	3	0	0	3	0
SPR_00394	tRNA links to Rfam database...	0.50	0.52	0.48	11	3632	17	6	6	5	10
SPR_00402	tRNA links to Rfam database...	0.76	0.76	0.76	16	2535	9	0	5	4	5
SPR_00434	tRNA links to Rfam database...	0.91	0.95	0.87	20	2827	3	3	0	0	1
SPR_00452	tRNA links to Rfam database...	0.67	0.76	0.59	16	2823	12	4	7	1	5
SPR_00595	tRNA links to Rfam database...	0.73	0.76	0.70	16	2752	8	3	4	1	5
SPR_00721	tRNA links to Rfam database...	0.93	0.90	0.95	19	2906	5	0	1	4	2
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...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00912	tRNA links to Rfam database...	0.48	0.52	0.44	11	2978	18	4	10	4	10
SPR_01157	tRNA links to Rfam database...	0.81	0.81	0.81	17	2754	6	0	4	2	4
SRP_00001	Bacteria_large_SRP links to Rfam database...	0.87	0.88	0.88	35	6746	6	1	4	1	5
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.60	0.60	0.60	15	2901	11	0	10	1	10
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.86	0.88	0.85	29	5531	6	1	4	1	4
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.19	0.18	0.21	6	5021	23	2	21	0	27
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.70	0.74	0.66	23	5530	14	1	11	2	8
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.45	0.48	0.43	12	3977	18	0	16	2	13
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.44	0.48	0.41	14	5016	23	4	16	3	15
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.89	0.88	0.90	28	6074	4	1	2	1	4
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	31	4721	2	0	1	1	1
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.30	0.30	0.31	9	5431	22	2	18	2	21
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.22	0.22	0.23	7	5534	24	3	21	0	25
SRP_00056	Bacteria_small_SRP links to Rfam database...	0.81	0.81	0.81	30	6404	8	1	6	1	7
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.73	0.74	0.72	26	6292	12	1	9	2	9
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5743	6	1	3	2	3
SRP_00067	Bacteria_small_SRP links to Rfam database...	0.68	0.66	0.71	25	5743	10	1	9	0	13
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.30	0.31	0.30	9	6298	27	1	20	6	20
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.16	0.17	0.16	5	6523	31	4	23	4	24
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.59	0.59	0.59	20	5531	16	1	13	2	14
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.24	0.24	0.24	9	6632	29	4	25	0	28
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.69	0.74	0.64	23	5529	13	1	12	0	8
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.86	30	5425	5	1	4	0	4
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.84	0.88	0.81	21	4069	7	1	4	2	3
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.85	0.88	0.81	22	3978	7	1	4	2	3
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.69	0.70	0.68	26	6403	14	1	11	2	11
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.29	0.29	0.29	10	5531	24	1	23	0	24
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.67	0.76	0.59	19	5221	16	5	8	3	6
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.13	0.16	0.12	3	3629	25	5	18	2	16
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.77	0.72	0.82	18	4256	7	0	4	3	7
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.76	0.81	0.73	29	6746	13	1	10	2	7
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.69	0.72	0.66	21	4819	14	0	11	3	8
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.55	0.55	0.55	16	5966	17	3	10	4	13
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.74	0.84	0.66	21	4154	11	4	7	0	4
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.94	0.95	0.93	39	6286	4	1	2	1	2
SRP_00145	Bacteria_small_SRP links to Rfam database...	0.96	0.98	0.95	39	6287	3	1	1	1	1
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5216	3	1	2	0	2
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.36	0.41	0.33	9	2823	18	5	13	0	13
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...	0.39	0.42	0.37	11	3456	19	4	15	0	15
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	33	6867	5	1	2	2	2
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.55	0.56	0.54	14	4069	13	0	12	1	11
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.77	0.81	0.74	17	3217	11	0	6	5	4
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.80	0.78	0.82	28	6869	7	1	5	1	8
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.63	0.59	0.67	16	4632	9	1	7	1	11
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.65	0.64	0.67	16	4162	10	1	7	2	9
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.82	0.80	0.83	20	3216	4	0	4	0	5
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.95	0.96	0.93	26	3375	3	1	1	1	1
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.94	0.96	0.92	23	3296	5	0	2	3	1
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.89	0.87	0.91	20	3299	4	0	2	2	3
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.94	0.96	0.92	24	3055	3	1	1	1	1
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.88	0.87	0.90	27	5121	3	1	2	0	4
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.32	0.33	0.31	9	5224	20	5	15	0	18
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.86	30	5425	6	1	4	1	4
SRP_00233	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	33	5118	0	0	0	0	0
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.95	0.90	1.00	28	5123	0	0	0	0	3
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.51	0.51	0.51	20	6864	19	3	16	0	19
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.78	0.81	0.76	29	6748	12	1	8	3	7
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.75	0.78	0.72	28	6982	14	1	10	3	8
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.72	0.72	0.72	21	4627	9	1	7	1	8
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.56	0.59	0.53	16	4156	15	4	10	1	11
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.59	0.61	0.59	20	5016	14	3	11	0	13
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.44	0.45	0.44	14	4624	18	2	16	0	17
SRP_00271	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3213	27	1	26	0	24
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.89	0.90	0.88	36	6745	7	1	4	2	4
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.93	0.95	0.92	36	6864	5	1	2	2	2
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.98	0.97	1.00	29	3712	0	0	0	0	1
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	37	6864	5	1	1	3	1
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.81	0.84	0.77	27	6635	10	1	7	2	5
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	5	0	3	2	3
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.41	0.37	0.45	10	4164	12	1	11	0	17
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...	0.87	0.87	0.87	20	2980	4	0	3	1	3
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.57	0.62	0.53	18	5322	16	5	11	0	11
SRP_00325	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	33	4338	0	0	0	0	0
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.56	0.55	0.59	17	5021	12	3	9	0	14
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.94	29	5120	2	0	2	0	5
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	35	5424	1	0	1	0	1
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.40	0.42	0.38	13	4719	21	3	18	0	18
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.59	0.60	0.58	15	3979	16	1	10	5	10
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.85	0.85	0.85	23	3889	5	1	3	1	4
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.83	0.80	0.86	24	5022	4	0	4	0	6
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	35	5319	4	1	1	2	1
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.93	0.91	0.94	32	6294	4	1	1	2	3
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.95	0.97	0.94	29	4722	5	0	2	3	1
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.96	0.96	0.96	26	3376	1	0	1	0	1
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.94	34	6750	3	1	1	1	1
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.89	0.89	0.89	31	5743	5	1	3	1	4
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.13	0.13	0.15	3	3220	17	4	13	0	21

^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 MXScarna(seed) - scored higher in this pairwise comparison

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

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

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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