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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:: AN ABSTRACT OF THE DISSERTATION OF Tai C. Hsu for the degree of

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:: ; max_pos = 18914; |P| = 8592; |T| = 14942; c = 2; IZ = 9; updates = 2907 Pattern: (in the middle) X. laevis

Creator:: Oregon State University. Dept. of Computer Science, Cull, Paul, 1943-, and Hsu, Tai C.
Abstract:: Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared characteristics. Most genetic string matching methods are based on the edit-distance model, which does not provide alignments for inversions and translocations. Recently, a heuristic called the Walking Tree Method [2, 3] has been...
Resource Type:: Research Paper
Full Text:: MATCH(Pi, Tj) = c if Pi = Tj MATCH(Pi, Tj) = 0 if Pi ≠ Tj For many of our examples we use c = 2. If we

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:: of my thesis to any reader upon request. e re Douglas C. ener, Redacted for Privacy Redacted

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