Computer Analysis of Sequence Data Part II

DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gener- ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods essen- tial to analysis, and a familiarity with computers and sequence analy- sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Computer Analysis of Sequence Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or pro- tein) sequences. Each chapter is written such that a competent scien- tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed prac- tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes encoun- tered by users of the sequence analysis software.