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Filtering by: Subject Hydraulics -- Data processing Resource Type Research Paper

Walking tree heuristics for biological string alignment, gene location, and phylogenies

Creator:

Oregon State University. Dept. of Computer Science, Cull, Paul, 1943-, Holloway, James Lee, and Cavener, Jeffrey Douglas

Abstract:

Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings...

Resource Type:

Research Paper

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in determining the sequential structure of DNA. Massive amounts of data on a variety of organisms are
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:

called text T. Our metaphor is to consider the data structure as a walking tree with |P| leaves, one