Table 2. The number of 10-mers needed to hit all 30-long sequences in four genomes: Two bacterial genomes A. tropicalis, C. crescentus, the worm C. elegans and a mammal genome, H. sapiens.
The genome sizes are quoted after removing all Ns and ambiguous codes. We tested three algorithms: minimizers picking the lexicographically smallest 10-mer, minimizer picking the first in a random k-mer ordering, and selection using the set produced by DOCKS. In case of multiple DOCKS-selected 10-mers in the 30-long window, the lexicographically smallest was chosen. # mers is the number of distinct 10-mers selected, and avg. dist. is the average distance between two selected 10-mers.
| Species | Genome size (Mbp) | Method | # mers (thousands) | avg. dist. |
|---|---|---|---|---|
| A. tropicalis | 0.393 | lexicographic | 32.9 | 9.48 |
| randomized | 28.0 | 11.0 | ||
| DOCKS | 23.7 | 12.4 | ||
| C. crescentus | 4 | lexicographic | 114.0 | 10.2 |
| randomized | 89.6 | 11.0 | ||
| DOCKS | 66.0 | 12.4 | ||
| C. elegans | 100 | lexicographic | 286.0 | 8.83 |
| randomized | 277.0 | 11.0 | ||
| DOCKS | 145.0 | 12.4 | ||
| H. sapiens | 2900 | lexicographic | 543.0 | 9.13 |
| randomized | 389.0 | 10.9 | ||
| DOCKS | 154.0 | 12.1 |