Efficient oligonucleotide probe selection for pan-genomic tiling arrays

BMC Bioinformatics

Table 2 Number of probes selected by PanArray to tile various bacterial pan-genomes.

Species	Strains	Avg. Length (Mbp)	Pan Length (Mbp)	Targets	Probes	Reuse
F. tularensis	14	1.88	26.29	1,355,504	121,312	11.2 (0.80)
S. aureus	14	2.88	40.38	2,006,144	200,999	10.0 (0.71)
B. anthracis	9	5.48	49.29	2,230,870	246,947	9.0 (0.99)
L. monocytogenes	20	2.74	54.81	2,832,489	358,688	7.9 (0.39)
V. cholerae	15	3.87	58.09	3,017,198	346,447	8.7 (0.58)
B. pseudomallei	20	6.72	134.31	6,755,234	491,231	13.8 (0.69)
E. coli/Shigella	29	4.96	143.72	8,210,679	674,697	12.2 (0.42)

Avg. length is the average genome length for a species. Pan length is the sum of all genome lengths for a species. Targets is the total number of locations targeted by the probes. A single probe may target multiple genomes in the species. Reuse is the average number of targets per probe, and a normalized reuse is given in parentheses as the reuse divided by the number of genomes.

ISSN: 1471-2105