Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

doi:10.1371/journal.pcbi.1000502

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

Figure 6

The branch closure.

The suffix interval [l‥r, h], representing some string of length h, is split into its children [l‥u, h+1], [u+1‥v, h+1] and [v+1‥r, h+1] by matching an additional character a∈{A, C, T}. We proceed building by matching the character C (solid bold green line). Beforehand, alternative suffix intervals are stored in , either representing mismatches (dashed red line), insertions (dashed dotted black line) or deletions (dotted blue line). holds suffix link intervals that in turn branch off from . The branch closure holds all such alternative intervals.

doi: https://doi.org/10.1371/journal.pcbi.1000502.g006