Searching for Endogenous Retroviral Proteins in the Mouse Genome

December 2011

Department of Computer Science, University of San Francisco

When a retrovirus becomes established in germ-line DNA, it becomes endogenous. At least eight percent of the human genome has been found to be of retroviral origin. Endogenous retroviral sequences have been found in many species. In our study, we search the mouse (murine) subset of the EST genome database for protein sequences from known murine retroviruses. We use BLAST search results with Phylogenetic Trees and Self-Organizing Maps to discover patterns and familial relationships between the sequences.

Team: Kristin Henry (project lead) and Ty Davis