Computational Analysis

T he development of the techniques of modern molecular biology, including PCR, cloning, and nucleotide sequencing, has revolutionized the practice of protein chemistry. Whereas the initial phase of detailed study of a new protein activity once involved chemical analysis of the amino acid sequence by Edman degradation of multiple fragments, it is more common today to establish a protein’s linear sequence from the nucleotide sequence of the gene that encodes it. While the number of new sequences reported based solely on classical protein sequence analysis has drastically declined, the molecular biology revolution has generated a rapidly expanding collection of new sequence data. The current efforts to sequence specific genomes in their entirety, including the human genome, will undoubtedly lead to further expansion of this information. Because linear sequence information is so readily available, computer methods for analyzing these data have also developed rapidly. This chapter will present methods for deriving important information on possible familial, structural, and functional relationships using only the linear sequence information as input.