A new method for analyzing protein sequence relationships based on Sammon maps

Recent advances in gene sequencing and rational drug design have re‐emphasized the need for new methods for protein analysis, classification, and structure and function prediction. In this article, we introduce a new method for analyzing protein sequences based on Sammon's non‐linear mapping algorithm. When applied to a family of homologous sequences, the method is able to capture the essential features of the similarity matrix, and provides a faithful representation of chemical or evolutionary distance in a simple and intuitive way. The merits of the new algorithm are demonstrated using examples from the protein kinase family.