Flexible and efficient genome tiling design with penalized uniqueness score

BMC Bioinformatics

Table 3 Design summary and coverage comparison

	Probe no.	Probe length^‡	Inter probe distance^‡	Base coverage	Window coverage
Agilent*	73373	53/52.85	202/426	11.11%	51.25%
-o −250^†	75036	60/57.16	246/411.9	12.29%	53.60%
-o −275	72087	60/57.11	269/431.1	11.80%	53.66%
-o −300	69491	60/57.02	292/449.4	11.35%	53.74%
-o −325	67074	60/56.92	313/467.7	10.94%	53.81%

* Agilent Human Whole Genome ChIP-on-Chip Set 244K (Chromosome 22 only).
† Overlapping size set to −250, probe length range [45, 60], Tm range [69, 74], U_p range [9, Inf), palindromic content range [0, 30%], GC content range [30%, 50%].
‡ Table cell is formatted as median/mean.
¶ Using the length of all unit-sized (1000 bp) windows in which at least one probe was placed.

ISSN: 1471-2105