Resolution:
## Figure 3.
Simplified example showing the calculation of shift values for 5-mers at the 3'-end. The 5-mers at the 3'-end of all sequences are extracted (A) and sorted by decreasing
frequency (B). The first 5-mer in the list (highest frequency) is then aligned to
the second 5-mer (C) to calculate the minimum number of shift operations to align
the two 5-mers without gaps (D). The shift direction is based on the 5-mer with the
higher frequency. Shifts to the left have negative values assigned, whereas shifts
to the right have positive values assigned. If the number of shift operations is less
than or equal to a given threshold (default: 2), then the two 5-mers are joined into
one k-mer. In the next step, the third 5-mer is aligned with either the first 5-mer or
the joined k-mer and the same operations are performed. These steps are repeated for the remaining
5-mers. The values of shift operations for the 3'-end are then adjusted (E) by the
negative of the maximum number of shift operations (- max{-1, 1}).
Schmieder |