CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		RNASampler(seed)
MCC	0.582	>	0.557
Average MCC ± 95% Confidence Intervals	0.551 ± 0.068	>	0.428 ± 0.070
Sensitivity	0.554	>	0.389
Positive Predictive Value	0.615	<	0.802
Total TP	897	>	630
Total TN	281881	<	282553
Total FP	751	>	215
Total FP CONTRA	76	>	48
Total FP INCONS	485	>	108
Total FP COMP	190	>	59
Total FN	721	<	988
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	897
Total TN	281881
Total FP	751
Total FP CONTRA	76
Total FP INCONS	485
Total FP COMP	190
Total FN	721

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.551 ± 0.068
Sensitivity	0.554
Positive Predictive Value	0.615
Nr of predictions	86

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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
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_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_00810	s2m links to Rfam database...	0.76	0.59	1.00	10	1071	0	0	0	0	7
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_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	12	0	0	12	0
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

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

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

Total Base Pair Counts
Total TP	630
Total TN	282553
Total FP	215
Total FP CONTRA	48
Total FP INCONS	108
Total FP COMP	59
Total FN	988

Total Scores
MCC	0.557
Average MCC ± 95% Confidence Intervals	0.428 ± 0.070
Sensitivity	0.389
Positive Predictive Value	0.802
Nr of predictions	86

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2. Individual counts for RNASampler(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...	0.88	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...	0.76	0.59	1.00	24	5026	0	0	0	0	17
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...	0.50	0.39	0.64	9	2687	6	0	5	1	14
PDB_00810	s2m links to Rfam database...	0.42	0.18	1.00	3	1078	0	0	0	0	14
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...	0.45	0.31	0.67	4	897	6	0	2	4	9
PDB_01092	glmS links to Rfam database...	0.72	0.62	0.84	32	10115	8	0	6	2	20
PDB_01152	HIV_FS2 links to Rfam database...	0.84	0.71	1.00	10	551	0	0	0	0	4
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...	0.63	0.40	1.00	6	1479	1	0	0	1	9
RFA_00433	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1425	1	0	0	1	9
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	5	0	0	5	0
RFA_00603	Telomerase-cil links to Rfam database...	0.63	0.51	0.78	18	13507	8	3	2	3	17
RFA_00604	Telomerase-cil links to Rfam database...	0.73	0.66	0.82	23	13502	14	4	1	9	12
RFA_00605	Telomerase-cil links to Rfam database...	0.41	0.31	0.55	11	15205	11	1	8	2	24
RFA_00607	Telomerase-cil links to Rfam database...	0.71	0.56	0.91	20	17744	9	0	2	7	16
RFA_00609	Telomerase-cil links to Rfam database...	0.82	0.68	1.00	25	17930	6	0	0	6	12
RFA_00610	Telomerase-cil links to Rfam database...	0.81	0.70	0.93	26	17177	9	0	2	7	11
RFA_00611	Telomerase-cil links to Rfam database...	0.68	0.57	0.80	20	13016	8	3	2	3	15
RFA_00613	Telomerase-cil links to Rfam database...	0.58	0.46	0.73	16	12858	6	4	2	0	19
RFA_00615	Telomerase-cil links to Rfam database...	0.63	0.51	0.78	18	13343	5	3	2	0	17
RFA_00632	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	4074	2	1	1	0	9
RFA_00636	HDV_ribozyme links to Rfam database...	0.85	0.75	0.95	21	3983	1	1	0	0	7
RFA_00642	Vimentin3 links to Rfam database...	0.58	0.39	0.88	7	2918	1	0	1	0	11
RFA_00643	Vimentin3 links to Rfam database...	0.21	0.17	0.27	3	2200	8	0	8	0	15
RFA_00644	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2691	4	1	3	0	12
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2403	12	3	9	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2135	4	1	3	0	12
RFA_00651	Vimentin3 links to Rfam database...	0.33	0.22	0.50	4	2072	4	1	3	0	14
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2133	12	3	9	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.39	0.28	0.56	5	2406	4	1	3	0	13
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...	0.53	0.29	1.00	4	986	0	0	0	0	10
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...	0.53	0.29	1.00	4	986	0	0	0	0	10
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...	0.46	0.21	1.00	3	4275	0	0	0	0	11
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	987	3	0	3	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...	-0.01	0.00	0.00	0	943	3	0	3	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00731	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00733	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00736	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00737	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00745	s2m links to Rfam database...	0.50	0.25	1.00	3	943	0	0	0	0	9
RFA_00749	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00758	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00762	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00763	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00764	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00765	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00767	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.52	0.39	0.70	7	2006	3	3	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.50	0.69	9	1940	4	4	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	3	0	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.85	0.72	1.00	23	5027	0	0	0	0	9
RFA_00786	Gammaretro_CES links to Rfam database...	0.79	0.63	1.00	20	5030	0	0	0	0	12
RFA_00791	Gammaretro_CES links to Rfam database...	0.71	0.56	0.90	18	5131	2	0	2	0	14
RFA_00792	Gammaretro_CES links to Rfam database...	0.81	0.72	0.92	23	5025	2	0	2	0	9
RFA_00801	Gammaretro_CES links to Rfam database...	0.74	0.63	0.87	20	5027	4	0	3	1	12
RFA_00808	RydC links to Rfam database...	0.58	0.56	0.60	9	2001	6	0	6	0	7
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

^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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

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

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

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