Exploration of Novel Methods to Visualize Genome Evolution

1. Exploration of Novel Methods to Visualize Genome Evolution Project Summary Last Year’s Highlights Reconstruction of the early history of life on Earth, including the order in which metabolic pathways were assembled. • Development of the new algorithm to select gene families http://bioinformatics.org/branchclust/ • Creation of software tool for the visualization of genome mosaicism from SOM maps. J. Peter Gogarten University of Connecticut gogarten@uconn.edu Lutz Hammel University of Rhode Island Maria Poptsova University of Connecticut Neha Nahar University of Rhode Island Plans for Next Year • Applications The developed tools facilitate the analysis of microbial genomes, especially with respect to the early evolution of life and the evolution of metabolic pathways. The work addresses questions central to NASA’s astrobiology program: “Understand how past life on Earth interacted with its changing planetary and Solar System environment” and “Understand the evolutionary mechanisms and environmental limits of life”. • Apply the SOM algorithm for embedded quartets. • Explore Principle Component Analysis (PCA) and Local Linear Embedding (LLE) algorithms. • Apply the analyses to different selection of genomes, with emphasis on those groups that might allow correlation to the fossil and geological records Keywords: Self Organizing Maps, Local Linear Embedding, Molecular Phylogeny, Early Evolution of Life, Astrobiology, Comparative Genome Analysis NASA AISRP 2004-07 http://gogarten.uconn.edu/AISRP