Kymberleigh Pagel

I will be working with Dr. Tiffani Williams in the Computer Science Department at Texas A&M from May 31 until August 5 2011. My graduate mentor is Suzanne Matthews. Our goal is to determine the evolutionary relationships of a set of cancer genes using phylogenetic trees.

The goal of the project is to look at the evolution of cancer genes. A selected set of cancer genes is collected and then multiple sequence alignments are performed to create a set of phylogenetic trees. By evaluating these trees via visualization and comparison the evolutionary history of a gene can be inferred (Final Report).
Step 0: Acquire data set of 16 genes over ten organisms. Review the selected genes. Determine if there is enough data to create accurate trees and fill in any missing data.
Step 1: Select a multiple sequence alignment tool and perform on the selected genes across organisms.
Step 2: Create an unrooted starting tree based upon results from Step 1 using random, NJ, or RSA.
Step 3: Perform phylogenetic search using TNT, MrBayes, and RAXML methods to determine sets of trees.
Step 4: Post-processing/Analysis of trees is performed using visualization and topographical comparison to draw conclusions about the evolutionary relationships of the genes.