Exploration of Novel Methods to Visualize Genome Evolution

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Exploration of Novel Methods to Visualize Genome
Evolution
Project Summary
Last Years 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_at_uconn.edu Lutz
Hammel University of Rhode Island Maria
Poptsova University of Connecticut Neha
Nahar University of Rhode Island
Plans for Next Year
Applications

• 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

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 NASAs 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.
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