A fast exact sequential algorithm for the partial digest problem

BMC Bioinformatics

Table 1 The Performance of the BBb2 algorithm for the restriction enzymes used in this study

Restriction enzyme	Restriction site	N	n	Time (Seconds)	Memory (MB)
NotI	GCGGCCGC	780	40	0.007	0.2
XbaI	TCTAGA	1891	62	0.017	3.6
SmaI	CCCGGG	103,285	455	56.2	8.9
BamHI	GGATCC	135,460	521	72	11.7
HindIII	AAGCTT	170,820	585	138.6	13.6
EcoRI	GAATTC	228,826	677	360	15.5
PvuII	CAGCTG	1,599,366	1789	24,012	98.8
EcoRV	GATATC	1,999,000	2000	42,840	979

Abbreviations: N is the number of cut fragments, n is the number of restriction sites

ISSN: 1471-2105