Computer Analysis of Amino Acid Sequences

Genome sequences are of minimal use without an adequate interpretation of the sequences of putative protein products, which is only possible on the basis of detailed computer analysis. The approaches to amino acid sequence analysis can be roughly divided into those that explore intrinsic properties of proteins, such as hydropathy, secondary structure, distribution of different types of amino acid sequences, and so on, and those that search for sequence similarity. Both approaches include numerous algorithms and computer programs. In this short chapter, we cannot describe all or even the most widely used and valuable of these methods. Instead, we present a minimal set of procedures that, in our experience, is useful in order to extract a substantial amount of information from an amino acid sequence in a relatively short time. For detailed descriptions of various computer methods for sequence analysis, the reader is referred to the recently published reviews and Methods in Enzymology collections (1–3).