Sequencing by Hybridization of Long Targets
Figure 3
Constructing the complete candidate set.
The algorithm first detects the locations of (l–1)-mer repeats in a single solution (leftmost column, repeats are shaded grey). Then we enumerate all possible extensions of the repeat (2nd column), continuing until we arrive at a set of candidate solutions that have the same length as the original sequence (3rd and 4th columns). Since all permutation of the subsequences between repeats are checked for consistency with the probe spectrum, all degenerate solutions are found.