Algorithms on Stings, Trees, and Sequences

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 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, essentiaUy independent of the biological environment the protein lives in. This assumption has recently been modified, but remains largely intact.