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In bioinformatics there are a great number of powerful computer tools available for the purpose of comparing genetic sequences. Perhaps the Google of genetic search tools is BLAST, which has been around since 1990 and is still among the most commonly used tools. In this and the next edition of Classroom Notes, we will take a look at 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, showing how one might employ Mathematica to illustrate these concepts in the classroom.
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