Investigation and Analysis of Context Dependent Mutation Rates Contribution to Synonymous Mutation Codon Usage via Development of CDMAP.

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Patton, D. (2022). Investigation and Analysis of Context Dependent Mutation Rates Contribution to Synonymous Mutation Codon Usage via Development of CDMAP. Unc Charlotte Electronic Theses And Dissertations.
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Abstract

Mutations play a pivotal role as a driver of genome evolution in organisms across the tree of life. However, site-specific mutation rates appear to have a non-uniform mutation rate and vary across the genome. Currently, site-specific variation has not been well characterized or analyzed using a uniform treatment. To address the lack of uniform analysis and provide an open-source, non-proprietary means of in-depth analysis, we developed the Context Dependent Mutation Analysis Pipeline (CDMAP for short). CDMAP is a novel pipeline that provides an automated, end-to-end, reproducible pipeline that provides in-depth analysis of genome-wide and replichore specific mutation rates and nucleotide triplet usage in bacterial prokaryotes. Additionally, we utilize the CDMAP pipeline to investigate patterns influencing genomic nucleotide triplets and synonymous codon usage through the lens of genomic GC content and various spatiotemporal factors.

Details
Author

Patton, David

Title

Investigation and Analysis of Context Dependent Mutation Rates Contribution to Synonymous Mutation Codon Usage via Development of CDMAP.

Physical Description

1 online resource (111 pages) : PDF

Date

2022

Degree Granting Institution

University of North Carolina at Charlotte

Abstract

Mutations play a pivotal role as a driver of genome evolution in organisms across the tree of life. However, site-specific mutation rates appear to have a non-uniform mutation rate and vary across the genome. Currently, site-specific variation has not been well characterized or analyzed using a uniform treatment. To address the lack of uniform analysis and provide an open-source, non-proprietary means of in-depth analysis, we developed the Context Dependent Mutation Analysis Pipeline (CDMAP for short). CDMAP is a novel pipeline that provides an automated, end-to-end, reproducible pipeline that provides in-depth analysis of genome-wide and replichore specific mutation rates and nucleotide triplet usage in bacterial prokaryotes. Additionally, we utilize the CDMAP pipeline to investigate patterns influencing genomic nucleotide triplets and synonymous codon usage through the lens of genomic GC content and various spatiotemporal factors.

Genre

doctoral dissertations

Subjects--Topics

Bioinformatics
Molecular biology
Biometry

Degree

Ph.D.

Keywords

Context Dependent Mutation
Evolutionary Biology
Mutation Accumulation
Mutation Rates
R Software
Visualization Tool

Subject Area

Bioinformatics

Advisor(s)

Sung, Way

Committee Members

Gibas, Cynthia
Rogers, Rebekah
Fodor, Anthony
Munir, Mariya

Degree Note

Thesis (Ph.D.)--University of North Carolina at Charlotte, 2022.

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Rights Holder Information

Copyright is held by the author unless otherwise indicated.

Identifier

Patton_uncc_0694D_13015

Permalink

http://hdl.handle.net/20.500.13093/etd:2735