Date of Award

Fall 2012

Degree Type

Thesis

Degree Name

Master of Science (MSc)

Department

Biology

Supervisor

Jonathan Dushoff

Language

English

Committee Member

Brian Golding, Paul Higgs

Abstract

We introduce new software (ISAAC: Improved Structural Annotation of attC) to annotate cassette arrays in bacterial integrons by finding attI and attC sites, and to provide detailed annotation of the attC sites for analysis. We demonstrate an initial application of ISAAC by annotating the cassette complements of all the integrons we identified in the RefSeq bacterial genome database, and providing an analysis of the patterns of nucleotide frequencies at the structurally important positions in the attCs we’ve found.

McMaster University Library

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