dc.contributor.author | Vey, Gregory | |
dc.date.accessioned | 2017-09-19 16:56:26 (GMT) | |
dc.date.available | 2017-09-19 16:56:26 (GMT) | |
dc.date.issued | 2017-09-19 | |
dc.date.submitted | 2017-06-09 | |
dc.identifier.uri | http://hdl.handle.net/10012/12401 | |
dc.description.abstract | The effective use of metagenomic functional interactions represents a key prospect for a variety of applications in the field of functional metagenomics. By definition, metagenomic operons represent such interactions but many operon predictions protocols rely on information about orthology and/or gene function that is frequently unavailable for metagenomic genes. In this thesis, I introduce the proposition of the proximon as a unit of functional interaction that is intended for use in metagenomic scenarios where supplemental information is sparse. The proximon is defined as a series of co-directional genes where minimal intergenic distance exists between any two consecutive member genes within the same proximon. In particular, the proximon is presented here as a biological abstraction aimed at facilitating bioinformatics and computational goals. In this thesis, proximons are constructed as information theoretic entities and employed in a variety of contexts related to functional metagenomics. I begin by implementing a computational representation for proximon data and demonstrate its utility through the deployment of a public database. Next, I perform a formal validation where proximons are contrasted against known operons by using the Escherichia coli K-12 model organism as a gold standard to measure the extent to which proximons emulate actual operons. This is followed by a demonstration of how proximon data can be applied to infer potential functional networks and depict potential functional modules. I conclude by enumerating the limitations of the research performed here and I present objectives and goals for future work. | en |
dc.language.iso | en | en |
dc.publisher | University of Waterloo | en |
dc.subject | bioinformatics | en |
dc.subject | genomics | en |
dc.subject | metagenomics | en |
dc.subject | functional interactions | en |
dc.title | The Proximon: Representation, Evaluation, and Applications of Metagenomic Functional Interactions | en |
dc.type | Doctoral Thesis | en |
dc.pending | false | |
uws-etd.degree.department | Biology | en |
uws-etd.degree.discipline | Biology | en |
uws-etd.degree.grantor | University of Waterloo | en |
uws-etd.degree | Doctor of Philosophy | en |
uws.contributor.advisor | Charles, Trevor | |
uws.contributor.affiliation1 | Faculty of Science | en |
uws.published.city | Waterloo | en |
uws.published.country | Canada | en |
uws.published.province | Ontario | en |
uws.typeOfResource | Text | en |
uws.peerReviewStatus | Unreviewed | en |
uws.scholarLevel | Graduate | en |