DNA Workbench

Abstract

In this paper we describe DNA Workbench, a program for working with DNA, RNA, and protein sequences. It is designed to solve several problems that arise in two domains. The first domain is that of the algorithm designer and implementor who is working in the emerging field of computational biology. The second domain is that of the worker in a genetics laboratory, who needs frequently to turn to the computer to perform analysis on existing or newly acquired nucleotide or protein sequences. The problems encountered in these two domains overlap to a considerable extent. The problems, and how they are addressed by DNA WorkBench, are discussed within. DNA WorkBench addresses both of these groups with one program. In this way, new problems that require new algorithms can be quickly brought from a theoretical solution to an implementation and to the laboratory workbench. This rapid transfer from research to development to the field is essential in a fast moving area such as biotechnology, by which term I mean to encompass such specialties as molecular biology, genetics, human gene therapy, and the current large-scale international sequencing and mapping of human DNA which has been organized as the Human Genome Project in the United States