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

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/n870zt26v

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  • 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 on the Walking Tree heuristics. I demonstrate my methods by showing a visual matching of mitochondrial genomes. I also show matchings based on amino acids and on hydrophobicity. I also show how the parameters of the visualization can be varied to produce more useful pictures. I implemented a parallel version of the Walking Tree heuristic and used it to produce a phylogenetic tree for picornaviruses. I also implemented several user interfaces. These programs are available on my WWW page which allows a user to produce a picture of a matching by giving the sequences in Gen Bank format and by making a few mouse clicks.
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  • File scanned at 300 ppi (Monochrome, 8-bit Grayscale, 24-bit Color) using ScandAll PRO 1.8.1 on a Fi-6670 in PDF format. CVista PdfCompressor 4.0 was used for pdf compression and textual OCR.
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  • description.provenance : Made available in DSpace on 2012-09-20T18:23:40Z (GMT). No. of bitstreams: 1 CavenerJeffreyDouglas1998.pdf: 8284113 bytes, checksum: c8ebbf1e122e0ff5d783913a94b77af9 (MD5) Previous issue date: 1997-08-11
  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2012-09-20T18:23:40Z (GMT) No. of bitstreams: 1 CavenerJeffreyDouglas1998.pdf: 8284113 bytes, checksum: c8ebbf1e122e0ff5d783913a94b77af9 (MD5)
  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2012-09-20T18:21:38Z (GMT) No. of bitstreams: 1 CavenerJeffreyDouglas1998.pdf: 8284113 bytes, checksum: c8ebbf1e122e0ff5d783913a94b77af9 (MD5)
  • description.provenance : Submitted by John Valentino (valentjo@onid.orst.edu) on 2012-09-19T22:14:23Z No. of bitstreams: 1 CavenerJeffreyDouglas1998.pdf: 8284113 bytes, checksum: c8ebbf1e122e0ff5d783913a94b77af9 (MD5)

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