Abstract
Abstract In the context of protein structure prediction, there are two principle reasons for comparing and aligning protein sequences: (a) To obtain an accurate alignment. This may be for protein modelling by comparison to proteins of known three-dimensional structure. (b) To scan a database with a newly determined protein sequence and identify possible functions for the protein by analogy with well-characterized 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.
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