Degenerate Primer Design via Clustering

  title={Degenerate Primer Design via Clustering},
  author={Xintao Wei and David N. Kuhn and Giri Narasimhan},
  journal={Proceedings. IEEE Computer Society Bioinformatics Conference},
This paper describes a new strategy for designing degenerate primers for a given multiple alignment of amino acid sequences. Degenerate primers are useful for amplifying homologous genes. However, when a large collection of sequences is considered, no consensus region may exist in the multiple alignment, making it impossible to design a single pair of primers for the collection. In such cases, manual methods are used to find smaller groups from the input collection so that primers can be… CONTINUE READING
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