ABSTRACT
With the continuing exponential growth in the number of sequences made available to the biologist, sequence alignment is an essential tool for sequence manipulation. These alignments have diverse applications in sequence assembly, annotation, and database searching as well as structural and functional predictions for proteins and genes, phylogenetic analysis, ancestral sequence reconstruction, and evolutionary analysis. These activities can be used for structure-based protein redesign to engineer proteins with desired novel function, to recreate ancestral proteins, or to create proteins with cross-reactive antigenic properties, which can span a group of proteins with diverse antigenic properties. This chapter examines some of the basic concepts involved in the manipulation of nucleotide sequences and applications of phylogenetics for protein engineering.
