Do you want to look at the whole genomic sequence or only predicted genes? Anyway, I would:

• Blast (blastx for whole genomic sequence, blastp for predicted protein coding genes, using a sensible cutoff e.g. 1e-6 or -10)
• IF looking for genes only, you simply select those without hits, done
• IF looking for all genomic regions, extract the blast HSP coordinates into subject-based ranges (chr, start, end), e.g. in bed or gff format, this can be done with bioperl (preferentially) or using the tabular blast format.
• load the regions into bed-tools or R and get all the gaps, that is regions with 0 coverage, when comparing to the chromosomes. If necessary, extend chromosome length to the real sequence length.