Gene discovery over multiple plasmids Ron Lev Shahar

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Gene discovery over multiple plasmids Ron Lev & Shahar Samocha Advisors: Prof. Michal Ziv-Ukelson,

Gene discovery over multiple plasmids Ron Lev & Shahar Samocha Advisors: Prof. Michal Ziv-Ukelson, Dr. Meirav Zehavi

The Uber-plasmid pattern discovery problem • Bacteria transfer genes over plasmids • Objectives: (1)

The Uber-plasmid pattern discovery problem • Bacteria transfer genes over plasmids • Objectives: (1) Discover gene complexes/pathways over multiple plasmids (2) Decipher unknown/uncharacterized genes by conserved context

Reduction to graph theory problem • Create Bipartite multigraph over two plasmidomes • Plasmids

Reduction to graph theory problem • Create Bipartite multigraph over two plasmidomes • Plasmids = Vertices, Shared genes = edges ' חיה א ' חיה ב Here, we solve a reduced version of the problem (two plasmids in each plasmidome)

Algorithm

Algorithm

Result: cross plasmid addiction module Pattern: A, B, G, H, J, L, U

Result: cross plasmid addiction module Pattern: A, B, G, H, J, L, U

Questions Bibliography: • • • Lathe III, W. C. , Snel, B. , &

Questions Bibliography: • • • Lathe III, W. C. , Snel, B. , & Bork, P. (2000). Gene context conservation of a higher order than operons. Trends in biochemical sciences, 25(10), 474 -479. Che, D. , Li, G. , Mao, F. , Wu, H. , & Xu, Y. (2006). Detecting uber-operons in prokaryotic genomes. Nucleic acids research, 34(8), 2418 -2427. Mruk, I. , & Blumenthal, R. M. (2008). Real-time kinetics of restriction–modification gene expression after entry into a new host cell. Nucleic acids research, 36(8), 2581 -2593.