Lossless filter for multiple repeats with bounded edit distance

Table 1 FINE/GOOD/EXCELLENT systematic comparison on MC58 sequence

RESTRICTION	NB. TESTS	EXCEL. SEL.	GOOD/FINE		EXCEL./GOOD		EXCEL./FINE
			SI	SD	SI	SD	SI	SD
overall	198	11.19	1.685	1.032	1.307	1.752	2.309	1.811
d/L ≥ 10%	99	18.45	2.302	1.043	1.508	2.062	3.428	2.166
d/L = 4%	99	3.93	1.067	1.021	1.107	1.441	1.191	1.467
q < 7	105	14.41	2.274	1.043	1.506	1.533	3.377	1.236
q ≥ 7	93	7.56	1.019	1.019	1.082	1.998	1.104	2.039
p/L ≥ 25%	159	5.90	1.820	1.033	1.347	1.321	2.546	1.236
p/L < 25%	39	32.77	1.135	1.027	1.146	3.506	1.347	3.614
p/L > 14%	183	8.99	1.720	1.031	1.312	1.415	2.363	1.457
p/L ≤ 14%	15	38.07	1.246	1.038	1.244	5.854	1.653	6.067
L = 200	69	6.42	1.958	1.044	1.456	1.744	2.829	1.835
L = 100	69	12.35	1.611	1.032	1.172	2.018	2.113	2.077
L = 50	60	15.35	1.454	1.019	1.292	1.454	1.938	1.479
r = 13	66	8.44	1.745	1.033	1.323	1.729	2.45	1.791
r = 8	66	11.11	1.677	1.032	1.302	1.756	2.280	1.817
r = 5	66	14.03	1.632	1.030	1.297	1.770	2.196	1.825
d/L ≥ 10%, p/L ≥ 25%	66	8.79	2.874	1.049	1.689	1.205	4.451	1.236
q < 7, d/L ≥ 10%	78	18.42	2.631	1.047	1.626	1.710	4.038	1.800
q < 7, d/L ≥ 25%	90	6.99	2.446	1.045	1.554	1.138	3.670	1.181
d/L ≥ 10%, p/L ≥ 25%, q < 7	63	8.78	2.962	1.050	1.722	1.188	4.614	1.237

Systematic comparison of FINE, GOOD and EXCELLENT on the MC58 data. Column nb. tests shows the number of set of parameters respecting the restriction context. Column Excel. sel. shows the absolute selectivity obtain thanks to method EXCELLENT. Using GOOD rather than FINE, we obtained an overall selectiveness improvement (SI) of plus 68% with a slowdown (SD) of only plus 3.2%. Using EXCELLENT rather than GOOD, for the cases with large errors (d/L ≥ 10%) and not too small threshold p (p/L ≥ 25%), the selectiveness improvement is of 69%, for a running time only 20.5% larger.

ISSN: 1748-7188