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Experiments with Algorithms for DNA Sequence Alignment

By Matt Lehman


A DNA sequence is a representation of the genetic code contained within an organism. Molecular biology researchers have great need to compare portions of DNA sequences. This paper discusses the computational problems inherent to this application, and shows how some solutions may be implemented. Global and local alignment implementations are presented. Known methods of quantifying global and local alignments are discussed and demonstrated. Dynamic programming techniques (using memoization through tabular computation) are discussed and applied to the implementations. As a background primer to these techniques, the concepts of ‘string edit distance ’ and ‘string edit transcripts ’ are discussed, and implementations to demonstrate them are presented. Background information is provided on the basics of DNA, the composition of DNA sequences, the motivations for DNA sequence alignment, and computational problems related to DNA sequence alignment

Year: 2009
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