<p> Three pieces of work are contained in this thesis. OGRe is a relational database
that stores mitochondrial genomes of animals. The database has been operational for
approximately five years and the number of genomes in the database has expanded
to over 1000 in this period. However, sometimes, new genomes can not be added to
the database because of small errors in the source ffies. Several improvements to the
update method and the organizational structure of OGRe have been done, which are
presented in the first part of this thesis. </p> <p> The second part of this thesis is a study on codon usage in mitochondrial genomes of mammals and fish. Codon usage bias can be caused by mutation and translational selection. In this study, we use some statistical tests and likelihood-based tests to determine which factors are most important in causing codon bias in mitochondrial
genomes of mammals and fish. It is found that codon usage patterns seem to be
determined principally by complex context-dependent mutational effects. </p> <p> The third part of this thesis is a phylogenetic study of 159 avian species obtained
using mitochondrial rRNA sequences that were provided by Dr. van Tuinen. In
this study, two methods are used: one considers sites of sequences as independently
evolving; the other includes the secondary structure of rRNAs. Unfortunately, the
amount of information in the rRNA sequences seems to be insufficient to determine the
whole phylogeny of birds. However, our results make it clear that several traditionally
defined orders are polyphyletic and therefore need to be redefined. </p> / Thesis / Master of Science (MSc)
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/21789 |
| Date | 12 1900 |
| Creators | Jia, Wenli |
| Contributors | Higgs, Paul, Computational Engineering and Science |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
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