On finding minimal absent words

BMC Bioinformatics

Table 3 Number of minimal absent words and generic absent words for some genomes.

Organism	Reference	Genome size			Length, n
			104	104	11
H. sapiens	Release 36.1	≈ 2.9 Gb	44 149	44 970	12
			2 039 862	2 368 682	13
			190	190	11
M. musculus	Release m36.1	≈ 2.6 Gb	52 087	53 573	12
			2 192 708	2 579 838	13
			104	104	11
D. melanogaster	FB 5	≈ 162 Mb	172 849	173 674	12
			10 040 282	11 335 034	13
			2	2	10
C. elegans	WB 170	≈ 100 Mb	7 664	7 680	11
			1 092 286	1 151 728	12
			2 262	2 262	11
N. crassa	Assembly 7	≈ 39 Mb	1 064 938	1 082 787	12
			20 213 298	27 903 272	13
			2	2	9
S. cerevisiae S228C	SGD 1	≈ 12 Mb	6 435	6 450	10
			414 520	462 882	11
			248	248	8
S. aureus MSSA476	NC002953	≈ 2.8 Mb	11 908	13 744	9
			162 113	251 497	10
			1	1	8
T. kodakarensis	NC006624	≈ 2.09 Mb	2 314	2 322	9
			136 917	154 340	10
			3	3	6
M. jannaschii	NC000909	≈ 1.66 Mb	126	150	7
			3 790	4 834	8
			5	5	6
M. genitalium	NC000908	≈ 0.58 Mb	340	380	7
			6 156	8 733	8

The notation corresponds to the number of minimal absent words of length n associated with string S, whereas has a similar meaning but for the case of generic absent words. The generic absent words have been generated using publicly available software provided by Herold et al. 3. The organisms are sorted according to decreasing genome size, which refers to the number of unambiguous bases of the genome. The reversed complement of the sequences has been considered in the generation of the results.

ISSN: 1471-2105