Pairwise Sequence Alignment

Pairwise alignment is often used to reveal similarities between sequences, determine the residue-residue correspondences, locate patterns of conservation, study gene regulation, and infer evolutionary relationships.

This chapter is divided into eight sections. It starts with a brief introduction in Section 3.1, followed by the dot matrix representation of pairwise sequence comparison in Section 3.2.

Using alignment graph, we derive a dynamic-programming method for aligning globally two sequences in Section 3.3. An example is used to illustrate the tabular computation for computing the optimal alignment score as well as the backtracking procedure for delivering an optimal global alignment.

Section 3.4 describes a method for delivering an optimal local alignment, which involves only a segment of each sequence. The recurrence for an optimal local alignment is quite similar to that for global alignment. To reflect the flexibility that an alignment can start at any position of the two sequences, an additional entry “zero” is added.