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  • Visualization, implementation, and application of the Walking Tree heuristics for biological string matching

    Creator:
    Cavener, Jeffrey Douglas
    Abstract:
    Biologists need tools to see the structural relationships encoded in biological sequences (strings). The Walking Tree heuristics calculate some of these relationships. I have designed and implemented graphic presentations which allow the biologist (user) to see these relations. This thesis contains background information on the biological sequences and some background...
    Resource Type:
    Masters Thesis
    Full Text:
    did not investigate this possibility. The first interface I designed was based on Tcl/Tk. The second

  • Walking tree methods for biological string matching

    Creator:
    Hsu, Tai C.
    Abstract:
    Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared characteristics. In contrast with the standard dynamic programming methods which use local edit distance models, the Walking Tree heuristic method was created to handle non-local changes, e.g., translocations, inversions, and duplications, altogether and...
    Resource Type:
    Dissertation
    Full Text:
    viruses into four families that were consistent with classifications based on other metrics. We also

  • Fast walking tree method via recurrence reduction for biological string alignment

    Creator:
    Oregon State University. Dept. of Computer Science, Hsu, Tai C., and Cull, Paul, 1943-
    Abstract:
    The meaning of biological sequences is a central problem of modern biology. Although string matching is well understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. To align biologically reasonable strings, we proposed the Walking Tree Method [4,5,6,7,8], an approximate string alignment method that...
    Resource Type:
    Research Paper
    Full Text:
    Most biological string matching methods are based on the edit-distance model [14] which assumes that