Introduction

In the context of protein structure prediction, there are two principle reasons for comparing and aligning protein sequences:

• To obtain an accurate alignment. This may be for protein modelling by comparison to proteins of known three-dimensional structure.

• To scan a database with a newly determined protein sequence and identify possible functions for the protein by analogy with well characterised proteins.

In this chapter I review the underlying principles and techniques for sequence comparison as applied to proteins and used to satisfy these two aims.