Understand the importance and usage of the hierarchical clustering using skew profiles.
Locate and process the viral cDNA genome files to calculate the skew profiles.
Understand the theory for using the Pythagorean equation to calculate the Euclidean distance. And apply that using python to build a linkage matrix.
Understand how errors occur, how to avoid them, and resolve their sources.
By the end of this project, you will create a Python program using a jupyter interface that analyzes a group of viruses and plot a dendrogram based on similarities among them. The dendrogram that you will create will depend on the cumulative skew profile, which in turn depends on the nucleotide composition. You will use complete genome sequences for many viruses including, Corona, SARS, HIV, Zika, Dengue, enterovirus, and West Nile viruses.
In a video that plays in a split-screen with your work area, your instructor will walk you through these steps:
Task 1: Getting Started with Hierarchical Clustering
Task 2: Locate and Process The Data Files
Task 3: Understand The Result Dataset
Task 4: Hierarchical Clustering - Metric
Task 5: Hierarchical Clustering - Ordering & Methods
Task 6: Dendrogram Plotting
Task 7: Dendrogram - Analysis
Task 8: Errors to Avoid
Your workspace is a cloud desktop right in your browser, no download required
In a split-screen video, your instructor guides you step-by-step
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