https://github.com/d-dawg78/comp561-final-project

McGill University - Computational Biology Methods and Research Project
https://github.com/d-dawg78/comp561-final-project

gene-evolution maximum-parsimony needleman-wunsch phylogenetic-trees sequence-alignment

Last synced: 9 days ago
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McGill University - Computational Biology Methods and Research Project

• Host: GitHub
• URL: https://github.com/d-dawg78/comp561-final-project
• Owner: d-dawg78
• Created: 2020-01-03T15:32:59.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2021-04-17T18:36:51.000Z (over 3 years ago)
• Last Synced: 2024-10-14T17:50:27.079Z (25 days ago)
• Topics: gene-evolution, maximum-parsimony, needleman-wunsch, phylogenetic-trees, sequence-alignment
• Language: Python
• Homepage:
• Size: 946 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
#### Final Project Submission for the Computational Biology Methods and Research course at McGill University!

#### Group: Dorian Desblancs

#### Introduction:

“Genes are rarely about inevitability, especially when it comes to humans, the brain, or behavior. They're about vulnerability, propensities, tendencies.”

― Robert M Sapolsky, Why Zebras Don't Get Ulcers

Elusive and mysterious, the Felidae family has been roaming this planet for longer than humans. Their lineage is diverse, and sprawls all continents and habitats. This report presents a phylogenetic study of three protein-coding genes present in the family’s species today: MT-COX1, MT-COX2, and MT-COX3. These genes are at the heart of the production of cytochrome c oxidase, an enzyme essential for breathing in all mammalian species. In this project, ancestral reconstructions of all three genes were generated. These were then analyzed to uncover the mysteries behind their evolution through time, and more importantly their adaptations to various environments.

In this report, some background information is first presented. This section notably introduces the Felidae family, cytochrome c oxidase and its role in mammals, and the gathering of nucleotide sequences for phylogenetic study. From there, the methodologies behind ancestral reconstruction and sequence comparison are outlined. The results produced by these methods are then displayed, interpreted and discussed.