The Changing Faces of Sequence Alignment: Overlap Alignment

Maximizing global alignment score

Earlier, we discussed how to use overlapping reads to assemble a genome, a problem that was complicated by errors in reads. Aligning the ends of the hypothetical reads shown below offers a way to find overlaps between error-prone reads.

An overlap alignment of strings ${v}$ = ${v}$$_{1}$ … ${v}_{n}$ ...