Identification of functional residues and secondary structure from protein multiple sequence alignment

This chapter describes a strategy for the hierarchical analysis of residue conservation and the identification of functional residues and secondary structure from protein multiple sequence alignment. Hierarchical methods of alignment cope with large numbers of sequences and give reasonably accurate alignments. Having generated the alignment, the problem is to find out what it can tell us about the protein family. Interpretation of alignments can be, particularly difficult when there are large numbers of sequences to examine. The method allows the residue-specific similarities and differences in physicochemical properties among groups of sequences to be identified quickly. The method also highlights conserved positions across a complete alignment and, thus, can help to identify patterns characteristic of regular secondary structures. The chapter also discusses a procedure for applying these patterns in secondary structure prediction and evaluates their predictive power in six blind secondary-structure predictions.