Abstract

The increasing abundance of genomic data has led to the creation of several databases containing the sequence data, metadata about the sequences and information about the organisms. These data are useful in many areas of biological research. Of the many available databases, few contain a significant amount of genome-associated data. In an effort to create a comprehensive microbial genomes database, the Genetic Elements of Microbes (GEM) database application was created. A K-mer analysis tool was also created and added the GEM application to provide an analysis of sequence composition and potential Lateral Gene Transfer (LGT) identification. The GEM application was designed to be convenient to maintain and extend. The K-mer analysis tool's ability to identify islands and to identify LGT events was tested with comparisons to published works. The GEM database application provides another source of genomic sequence and genome-associated data for the scientific community. The K-mer analysis addition provides an easy-to-customize tool to identify regions of dissimilarity and identify potential LGT events. The GEM application interface is publicly accessible at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/GEMSearch.cgi. The standalone K-mer analysis interface is available at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/KmerAnalysis.cgi.

Library of Congress Subject Headings

Microbial genetics--Data processing; Genomics--Data processing; Database management

Publication Date

5-1-2009

Document Type

Thesis

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Johnson, Justin

Advisor/Committee Member

Skuse, Gary

Comments

Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works. Physical copy available through RIT's The Wallace Library at: QH434 .B46 2009

Campus

RIT – Main Campus

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