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There are a great number of powerful computer tools available for the purpose of comparing genetic sequences. The Google of genetic search tools is BLAST, which has been around since a and is still among the most commonly used tools. In this and the previous edition of Classroom Notes, we examine some of the basic ideas that go into the alignment of nucleotide sequences, such as the dot matrix and the algorithms of Needelman-Wunsch and Smith-Waterman. We also show how one might employ Mathematica to illustrate these concepts in the classroom.
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