Evaluation and improvements in the automatic alignment of protein sequences

The accuracy of protein sequence alignment obtained by applyinga commonly used global sequence comparison algorithm is assessed.Alignments based on the superposition of the three-dimensionalstructures are used as a standard for testing the automatic,sequence-based methods. Alignments obtained from the globalcomparison of five pairs of homologous protein sequences studiedgave 54% agreement overall for residues in secondary structures.The inclusion of information about the secondary structure ofone of the proteins in order to limit the number of gaps insertedin regions of secondary structure, improved this figure to 68%.A similarity score of greater than six standard deviation unitssuggests that an alignment which is greater than 75% correctwithin secondary structural regions can be obtained automaticallyfor the pair of sequences.