Three Dimensional Phylogenetic Relationships:
How changes in dimensional representation can influence visual relationships.
In this exercise you will learn to -
- Use the SDSC Biology WorkBench to find a protein of interest and compare it with other related proteins.
- Construct a phylogenetic tree with ClustalW in Biology WorkBench that shows the relationships of the proteins in 2-D space.
- Transform a distance matrix created in CLUSTALW into a 3-D phylogenetic tree.
- Compare the 2-D and 3-D trees and think about the spatial relationships.
Exercise Overview -
- Create an account in Biology WorkkkBench
- Start a new session with "Protein Tools"
- Select a data set (10 proteins that are of interest to you)
- Create a phylogenetic tree with CLUSTALW
- Transform your tree into a distance matrix
- Export that matrix into MATLAB
- Run special" whiz bang" program created by Gretchen that transforms the matrix into 3-D spatial relationships.
- Compare the 2-D CLUSTALW tree to the 3-D graphed relationships of selected points on that tree.
- Generally become a lot smarter and consequently better person!
Exercise Bifurcation -
- Produce Your Own Data and perform all of the manipulations individually.
- Use Pre-Packaged Data for an exercise overview.