History and motivation

Although I didn't know it at the time, I began writing this book in the summer of 1988 when I was part of a computer science (early bioinformatics) research group at the Human Genome Center of Lawrence Berkeley Laboratory. Our group followed the standard assumption that biologically meaningful results could come from considering DNA as a one-dimensional character string, abstracting away the reality of DNA as a flexible three-dimensional molecule, interacting in a dynamic environment with protein and RNA, and repeating a life-cycle in which even the classic linear chromosome exists for only a fraction of the time. A similar, but stronger, assumption existed for protein, holding, for example, that all the information needed for correct three-dimensional folding is contained in the protein sequence itself, essentially independent of the biological environment the protein lives in. This assumption has recently been modified, but remains largely intact [297].

For nonbiologists, these two assumptions were (and remain) a god send, allowing rapid entry into an exciting and important field. Reinforcing the importance of sequence-level investigation were statements such as: