Genolve : a bioinformatics tool for the study of structure-driven genome evolution
Date
2021-04
Authors
Journal Title
Journal ISSN
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Publisher
Stellenbosch : Stellenbosch University
Abstract
ENGLISH SUMMARY : The process of structural genomic evolution, how one genome may have evolved into another via large-scale rearrangement events, has been a topic of study for the last few decades. Numerous
genomic sorting models and algorithms that transform one genome into another using genome
rearrangements exist. From a biological perspective, some of the models are more accurate than
others. The rDCJ model is currently the best in this respect. In order to gain an in-depth
understanding of the underlying mechanisms of genome evolution, knowledge of the different
ways in which one genome may have evolved into another, is vital. At present, bioinformatic tools
do exist that implement one or more of the genomic sorting models, however they output only one
of an often-vast amount of equiprobable rearrangement scenarios.
This thesis describes amendments made to the existing rDCJ genomic sorting model, which
increases its biological accuracy. The amended model was incorporated into an algorithm that
finds all of the most parsimonious rearrangement scenarios for sorting one genome into another.
This allowed for the development of the open-source, command-line, bioinformatics tool,
Genolve.
When tested on simulated data, Genolve transformed one input genome into another 100% of the
time, generating the full set of the most parsimonious sorting scenarios in its output. Unique to
Genolve is also an output-summary of the average number and type of rearrangements present in
the set of rearrangement scenarios. Application to two related strains of the yeast, Saccharomyces
cerevisiae, illustrated the utility of the tool in analysing biological data.
Making Genolve available as an open-source tool will allow researchers interested in the process
of genomic evolution to conduct comprehensive studies in greater depth than was previously
possible.
AFRIKAANSE OPSOMMING : Geen opsomming beskikbaar.
AFRIKAANSE OPSOMMING : Geen opsomming beskikbaar.
Description
Thesis (MSc)--Stellenbosch University, 2021.
Keywords
Genolve, Genomics -- Analysis, Bioinformatics, Saccharomyces cerevisiae -- Genetic engineering, Evolutionary genetics, UCTD