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Finding "corresponding" genes
How to identify “corresponding” genes across species
Genes in two species that originated from the same ancestral gene in the last common ancestor of the species are good candidates for being 'corresponding' genes (orthologs)
Orthologs are genes in two species that are mutually most similar to each other
Analysis
In this course, we will follow the steps of a comparative genomics analysis of plant cell wall degrading enzymes (PCDs). Plant cell walls are made up of cellulose and hemi-cellulose, making them two of the most common organic molecules on Earth and key components of the carbon cycle.
It was thought for a long time that PCDs are only produced by fungi and certain bacteria, but in recent years, evidence has accumulated that some invertebrate animals may be able to degrade plant cell walls as well.
To find out how widespread the ability to degrade plant cell wall, really is we trace the distribution of 235 potential PCDs across all eukaryotic datasets available in the RefSeq database.
Task 1: Exploration
- Open a visualizaiton of the results generated using this interactive web-viewer
- Wait a moment for the data to load. Once you were redirected to the “Main profile” page, select a taxonomic rank and click the red PLOT button
- Explore the “Main plot” on different taxonomic levels
- Select the “Dimension reduction” plot from the top menu and explore the plot with “Phylum”-level labels
Task 2: Finding corresponding genes
After having explored the results, let's find out how they were generated. Have another look at the assumptions at the top of the page.