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Bacteriophage Gene Clustering and Phylogeny

Bacteriophage Gene Clustering and Phylogeny. Nicholas Celms San Diego State University Funded in part by NSF 0827278 UBM Interdisciplinary Training in Biology and Mathematics. Goal.

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Bacteriophage Gene Clustering and Phylogeny

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  1. Bacteriophage Gene Clustering and Phylogeny Nicholas Celms San Diego State University Funded in part by NSF 0827278 UBM Interdisciplinary Training in Biology and Mathematics.

  2. Goal • Build a method for making taxonomic groupings of bacteriophages based on sets of protein-encoding genes (PEGs)

  3. Bacteriophages • Viruses that infect bacteria • ~24-200 nm long • Horizontal gene transfer • Short, highly-diverse genomes

  4. Goal • Build a method for making taxonomic groupings of bacteriophages based on sets of protein-encoding genes (PEGs) • Define clusters of protein-encoding genes that differentiate strains of bacteriophages into subdivisions called clans • Define super-groups of clans called components • Examine components and clans for: • phylogeny • Classification of new strains • Use PEG clusters to: • Improve functional annotations • Define lifestyle indicators • Find horizontally-transferred groups of genes

  5. Clustering Strains

  6. Focusing on one clan

  7. Image Cluster: PEG set associated with clan

  8. Image Cluster vs. Clusters Image cluster: generic PEG set associated with a clan Cluster: a phage’s specific set of PEG orthologs of the image cluster

  9. Data 120 phages, 8558 PEGs Filtered: 2512 contributive PEGs (appear in a cluster) 335 clans (interrelated groupings of phages) forming 14 components

  10. Results

  11. Future • Broadening our analysis to all available phages • ~700 phages, ~55,000 PEGs • Phage phylogeny • Experimentally-validating suggested functional annotations

  12. Questions?

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