Pairwise sequence alignment

This chapter is about sequence similarity. Let us start with a warning: there is no unique, precise, or universally applicable notion of similarity. An alignment is an arrangement of two sequences which shows where the two sequences are similar, and where they differ. An optimal alignment, of course, is one that exhibits the most similarities, and the least differences. Broadly, there are three categories of methods for sequence comparison.

• Segment methods compare all overlapping segments of a predetermined length (e.g., 10 amino acids) from one sequence to all segments from the other. This is the approach used in dotplots.
• Optimal global alignment methods allow the best overall score for the comparison of the two sequences to be obtained, including a consideration of gaps.
• Optimal local alignment algorithms seek to identify the best local similarities between two sequences but, unlike segment methods, include explicit consideration of gaps.