Overlap alignment

An overlap alignment of strings $s$ and $t$ is a local alignment that demands we align a suffix of $s$ with a prefix of $t$. We therefore aim to maximize some alignment score over all such substrings of $s$ and $t$ (where we may require the prefix and suffix to have some minimal length).

Overlap alignment is particularly useful in genome sequencing, where errors in reads makes finding exact overlaps in reads an impractical aim and alignment is preferable.

The term "overlap alignment" has also been used to describe what Rosalind defines as a semiglobal alignment.