Chapter 3: Alignment of Pairs of Sequences

Knowing how to align a pair of nucleic acid or protein sequences is a fundamentally important area of bioinformatics. For very similar sequences with runs of identical or commonly found substitutions, this is quite readily done; but as the sequences become more divergent, they also become more difficult to align. Thus, a method is required to find the very best possible or optimal alignment given an expected pattern of variation in sequences that are related but have also diverged over evolutionary time. Even if such requirements are met, human judgment may have to be used because there may be more than one possible alignment and some regions may align much better than others, leaving the poorly aligning regions in doubt. This chapter discusses how to perform pair-wise sequence alignments and how to score these alignments. The chapter following this one describes how to evaluate the significance of alignment scores.