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Dissertation/Thesis Abstract

Finding duplication events using GenomeVectorizer
by Kochetkova, Elena, M.S., San Jose State University, 2010, 58; 1488131
Abstract (Summary)

GenomeVectorizer is a software application designed to extend the functionality of GenomePixelizer, a genome-visualization tool that was developed for the Department of Plant Pathology at University of California, Davis, in 2002. GenomeVectorizer was written using XML, XSLT, and SVG technologies combined with JavaScript scripting to provide the level of flexibility, dynamism, and interactivity not supported by the TCL/TK written application (GenomePixelizer). This new visualization tool was tested with available data from the Arabidopsis NBS-LRR study, and its output was compared to the output of GenomePixelizer. The relationships drawn at the same identity value were identical.

GenomeVectorizer was successfully applied to study NBS-LRR genes and duplication events in Glycine max (soybean). The images of NBS-LRR genes were generated at 50, 60, and 70 percent identity. Images also showed the relationships between the duplication events. At a glance, it was easy to determine that duplication regions include almost half of the genome.

Currently, the user can generate an image at a specified percent identity, highlight gene relationships by clicking on the identity value inside the identity matrix, visit a gene’s database entry, and drag chromosomes away from each other.

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Indexing (document details)
Advisor: Lin, Tsau Y.
Commitee: Louie, Eric, Martin, Johnny
School: San Jose State University
Department: Computer Science
School Location: United States -- California
Source: MAI 49/03M, Masters Abstracts International
Subjects: Genetics, Bioinformatics, Computer science
Keywords: Finding genome duplication events, Genome duplication, Genome visualization, Scientific visualization, Visualization
Publication Number: 1488131
ISBN: 978-1-124-43477-3
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