CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	HotKnots		Murlet(seed)
MCC	0.570	>	0.483
Average MCC ± 95% Confidence Intervals	0.538 ± 0.071	>	0.352 ± 0.082
Sensitivity	0.560	>	0.283
Positive Predictive Value	0.586	<	0.828
Total TP	939	>	475
Total TN	253779	<	254807
Total FP	807	>	103
Total FP CONTRA	90	>	0
Total FP INCONS	573	>	99
Total FP COMP	144	>	4
Total FN	737	<	1201
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of HotKnots and Murlet(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 HotKnots and Murlet(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 HotKnots and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for HotKnots and Murlet(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 HotKnots and Murlet(seed)).

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	939
Total TN	253779
Total FP	807
Total FP CONTRA	90
Total FP INCONS	573
Total FP COMP	144
Total FN	737

Total Scores
MCC	0.570
Average MCC ± 95% Confidence Intervals	0.538 ± 0.071
Sensitivity	0.560
Positive Predictive Value	0.586
Nr of predictions	88

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2. Individual counts for HotKnots [ 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_00213	Gammaretro_CES links to Rfam database...	0.92	0.85	1.00	35	5015	0	0	0	0	6
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	2678	24	1	22	1	23
PDB_00810	s2m links to Rfam database...	0.71	0.65	0.79	11	1067	4	0	3	1	6
PDB_01050	UnaL2 links to Rfam database...	0.96	0.92	1.00	12	618	2	0	0	2	1
PDB_01051	Telomerase-cil links to Rfam database...	0.75	0.69	0.82	9	892	6	0	2	4	4
PDB_01092	glmS links to Rfam database...	0.69	0.65	0.74	34	10107	13	0	12	1	18
PDB_01152	HIV_FS2 links to Rfam database...	0.92	0.86	1.00	12	549	0	0	0	0	2
RFA_00390	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...	0.93	0.93	0.93	14	1470	4	0	1	3	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	12	0	0	12	0
RFA_00603	Telomerase-cil links to Rfam database...	0.64	0.69	0.60	24	13490	19	4	12	3	11
RFA_00604	Telomerase-cil links to Rfam database...	0.72	0.74	0.70	26	13493	22	2	9	11	9
RFA_00605	Telomerase-cil links to Rfam database...	0.37	0.34	0.40	12	15195	27	3	15	9	23
RFA_00611	Telomerase-cil links to Rfam database...	0.63	0.63	0.63	22	13006	15	3	10	2	13
RFA_00613	Telomerase-cil links to Rfam database...	0.61	0.60	0.62	21	12846	15	4	9	2	14
RFA_00615	Telomerase-cil links to Rfam database...	0.51	0.51	0.51	18	13331	17	8	9	0	17
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	2	17	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00642	Vimentin3 links to Rfam database...	0.16	0.17	0.17	3	2908	15	1	14	0	15
RFA_00643	Vimentin3 links to Rfam database...	0.20	0.22	0.20	4	2191	16	1	15	0	14
RFA_00644	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2676	25	6	19	0	18
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2394	21	4	17	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.34	0.33	0.35	6	2128	13	2	9	2	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	11	3	8	0	12
RFA_00654	Vimentin3 links to Rfam database...	0.27	0.28	0.28	5	2397	13	2	11	0	13
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	1120	10	1	7	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...	0.42	0.36	0.50	5	1118	6	0	5	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.71	0.71	0.71	10	1114	5	0	4	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...	0.42	0.43	0.43	6	976	9	0	8	1	8
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...	0.74	0.71	0.77	10	1115	6	0	3	3	4
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...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00695	Hammerhead_1 links to Rfam database...	0.56	0.50	0.64	7	7010	29	1	3	25	7
RFA_00703	Hammerhead_1 links to Rfam database...	0.67	0.64	0.69	9	4265	18	1	3	14	5
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	976	14	2	12	0	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...	0.29	0.29	0.31	4	1022	10	0	9	1	10
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	3	6	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.30	0.29	0.33	4	1023	10	0	8	2	10
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	10	0	9	1	14
RFA_00710	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	9	0	9	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	10	0	9	1	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	936	10	0	10	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	935	11	0	11	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...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00733	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00734	s2m links to Rfam database...	0.61	0.67	0.57	8	889	7	1	5	1	4
RFA_00736	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00737	s2m links to Rfam database...	0.75	0.75	0.75	9	891	5	0	3	2	3
RFA_00745	s2m links to Rfam database...	0.66	0.67	0.67	8	934	5	1	3	1	4
RFA_00749	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00758	s2m links to Rfam database...	0.63	0.58	0.70	7	893	3	1	2	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...	0.75	0.75	0.75	9	891	4	0	3	1	3
RFA_00764	s2m links to Rfam database...	0.66	0.67	0.67	8	891	5	1	3	1	4
RFA_00765	s2m links to Rfam database...	0.75	0.75	0.75	9	891	5	0	3	2	3
RFA_00767	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1870	3	3	0	0	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	21	0	19	2	18
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1999	20	0	17	3	18
RFA_00773	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	22	0	19	3	18
RFA_00779	Corona_pk3 links to Rfam database...	0.87	0.94	0.81	17	1932	4	3	1	0	1
RFA_00781	Gammaretro_CES links to Rfam database...	0.58	0.59	0.58	19	5017	14	2	12	0	13
RFA_00786	Gammaretro_CES links to Rfam database...	0.71	0.72	0.70	23	5017	10	2	8	0	9
RFA_00791	Gammaretro_CES links to Rfam database...	0.35	0.34	0.35	11	5120	20	5	15	0	21
RFA_00792	Gammaretro_CES links to Rfam database...	0.94	0.94	0.94	30	5018	4	0	2	2	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.85	0.81	0.90	26	5021	4	0	3	1	6
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.74	0.84	0.66	21	4154	13	4	7	2	4
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.91	0.90	0.93	37	6288	3	1	2	0	4
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5216	3	1	2	0	2
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.91	0.87	0.96	26	3714	1	0	1	0	4
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.94	0.94	0.94	34	5424	2	0	2	0	2

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

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

Total Base Pair Counts
Total TP	475
Total TN	254807
Total FP	103
Total FP CONTRA	0
Total FP INCONS	99
Total FP COMP	4
Total FN	1201

Total Scores
MCC	0.483
Average MCC ± 95% Confidence Intervals	0.352 ± 0.082
Sensitivity	0.283
Positive Predictive Value	0.828
Nr of predictions	88

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2. Individual counts for Murlet(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...	0.53	0.29	1.00	4	942	2	0	0	2	10
PDB_00012	mir-TAR links to Rfam database...	0.65	0.43	1.00	3	403	0	0	0	0	4
PDB_00213	Gammaretro_CES links to Rfam database...	0.73	0.59	0.92	24	5024	2	0	2	0	17
PDB_00553	mir-TAR links to Rfam database...	0.45	0.27	0.75	3	461	1	0	1	0	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.23	0.13	0.43	3	2694	4	0	4	0	20
PDB_00810	s2m links to Rfam database...	0.63	0.53	0.75	9	1069	3	0	3	0	8
PDB_01050	UnaL2 links to Rfam database...	0.55	0.31	1.00	4	626	1	0	0	1	9
PDB_01051	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
PDB_01092	glmS links to Rfam database...	0.69	0.48	1.00	25	10128	0	0	0	0	27
PDB_01152	HIV_FS2 links to Rfam database...	0.76	0.64	0.90	9	551	1	0	1	0	5
RFA_00390	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_00433	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	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_00603	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00604	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00605	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	15225	0	0	0	0	35
RFA_00611	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13041	0	0	0	0	35
RFA_00613	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	35
RFA_00615	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13366	0	0	0	0	35
RFA_00632	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	4088	4	0	4	0	25
RFA_00636	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	3998	4	0	4	0	25
RFA_00642	Vimentin3 links to Rfam database...	0.57	0.44	0.73	8	2915	3	0	3	0	10
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2203	8	0	8	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.42	0.33	0.55	6	2690	5	0	5	0	12
RFA_00645	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2407	8	0	8	0	18
RFA_00649	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00651	Vimentin3 links to Rfam database...	0.42	0.33	0.55	6	2069	5	0	5	0	12
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.57	0.44	0.73	8	2404	3	0	3	0	10
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00659	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00695	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4278	0	0	0	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00706	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00709	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	0	0	0	0	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00767	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1882	3	0	3	0	12
RFA_00768	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1883	3	0	3	0	13
RFA_00769	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	1942	3	0	3	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	2005	3	0	3	0	10
RFA_00773	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1945	3	0	3	0	13
RFA_00779	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1944	3	0	3	0	12
RFA_00781	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00786	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00791	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5125	2	0	2	0	8
RFA_00792	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00801	Gammaretro_CES links to Rfam database...	0.80	0.72	0.88	23	5024	3	0	3	0	9
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	6	4180	0	0	0	0	19
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.35	0.12	1.00	5	6323	1	0	0	1	36
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5247	0	0	0	0	30
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	6	3735	0	0	0	0	24
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5454	0	0	0	0	30

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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

Table of contents:

Overview

Performance plots

Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

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

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

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

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