Implementing Pairwise Alignments in Bioinformatics with Computer Algebra

Newcomers to the field of bioinformatics are faced with a bewildering array of databases and tools, which use a variety of interfaces and data formats. This observation notwithstanding, an increasing number of universities now offer bioinformatics courses and majors. This paper provides a simple and inexpensive alternative to these complex databases and tools for teaching an introductory course in bioinformatics. It describes how the computer algebra package, Maple, can be used in an introductory bioinformatics course, to illustrate the concepts and methods by which alignments between two related nucleotide or polypeptide sequences can be found and evaluated. Emphasis is placed on visualizing the alignments using two and three-dimensional graphics