``Understanding the laws of nature does not mean that we are immune to their operations.'' (Solomon Short)
This chapter is meant to be a short introduction to the chemical, biological and computational aspects of sequencing and assembly. It presents and formally defines the problem of genome and EST sequencing while introducing the terminology as it is used throughout this thesis. This chapter cannot be an exhaustive reference to sequencing methods, DNA properties or biological background information at large, some facts have been simplified to clarify the context. See for example DOE (1992), Bruce et al. (1994) or Klug and Cummings (1996) for more advanced information.