Visualization, implementation, and application of the Walking Tree heuristics for biological string matching
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...
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| Language: | en_US |
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2012
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| Online Access: | http://hdl.handle.net/1957/33688 |
| Summary: | 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. === Graduation date: 1998 |
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