Senior Honors Projects, 2010-2019
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This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Date of Graduation
Spring 2017
Document Type
Thesis
Degree Name
Bachelor of Science (BS)
Department
Department of Biology
Advisor(s)
Steven G. Cresawn
Jonathan Monroe
Morgan Steffen
Abstract
Horizontal gene transfer plays a large role in microbial genetic diversity. Bacteriophages can mediate diversity within their hosts through transduction, the uptake and dispersal of microbial host DNA between bacterial hosts. However, bacteriophages themselves experience horizontal gene transfer through mobile genetic elements and recombination. Unlike their hosts, bacteriophages cannot easily be mapped onto a phylogenic tree as they do not all possess a common trait like the 16s RNA gene. However, their genomes are typically small enough to be analyzed usingThere are tools to compare bacteriophages such as Gepard and Phamerator that compare nucleotide identity across bacteriophage entire genomes. However, Gepard lacks the ability to contextualize the analysis with respect to annotated genes, , but none that fully capture evidence of horizontal gene transfer and display it in an intuitive manner. and Phamerator, by its very nature as a comparison tool, cannot highlight repeats within a single genome. Programs Many programs to identify repeat motifs also exist, but many lack the ability to display genomic information and regard repeats in an isolated manner. To address this problem, I have developed Repeaterator, a tool to visualize DNA repeat motifs within Actinobacteriophage genomes. Much like Phamerator, Repeaterator displays bacteriophage genomes and their annotations visually using the D3.js library from a Mongo database. Instead of comparing multiple genomes, Repeaterator compares a genome to itself to map the occurrence of DNA repeat motifs in the context of gene annotations. Additionally, other genomic information can easily be overlaid on the visualization, including GC content or the strand the gene is coded on. Repeaterator provides powerful new insight into the evolutionary origins of Actinobacteriophage genomes and can easily be easily adapted to analyze other genomes. Much like Phamerator, Repeaterator displays bacteriophage genomes and their annotations visually using the D3.js library from a Mongo database.as an interactive data visualization. It uses the same underlying technologies as Phamerator itself and will be available along with our other tools on http://phamerator.org for general use.
Recommended Citation
Rybnicky, Grant A., "Repeaterator: A tool for visualizing DNA repeat motifs in actinobacteriophage genomes" (2017). Senior Honors Projects, 2010-2019. 272.
https://commons.lib.jmu.edu/honors201019/272
