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Identifying probable prophage DNA in mycobacterial genomes

Identifying probable prophage DNA in mycobacterial genomes. Bobby Chaggar BNFO 301 Lysogeny Group. Experimental Design. Compare (SEQUENCE-SIMILAR-TO) each lysogenic, mycobacteriophage to a list of all mycobacteria in BioBIKE ( PhAnToMe )

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Identifying probable prophage DNA in mycobacterial genomes

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  1. Identifying probable prophageDNA in mycobacterial genomes Bobby Chaggar BNFO 301 Lysogeny Group

  2. Experimental Design Compare (SEQUENCE-SIMILAR-TO) each lysogenic, mycobacteriophage to a list of all mycobacteria in BioBIKE (PhAnToMe) From the highest hit against each unique bacterium, compare the associated bacterial protein against *all-phages* If a set of phages have similar levels of homology, analysis of attachment sites is undergone, along with a GC content analysis to best predict major prophage sequences

  3. Result • Example: Comparison of Mycobacterium-phage-Tweety • 43.6% ID (e-value = 8.00e-100) with Mycobacterium-Marinum-M’s p3540 • Outranked by several phages, namely Mycobacterium-Phage-Pacc40, 43.8% ID (e-value = 1.0e-100) • Subject to attachment site and GC content analysis • Continue examining the rest of the mycobacteriophages

  4. Ex. Sequence similarity with mycobacterium marinium M.

  5. References “PHAST: A Fast Phage Search Tool.” You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis and David S. Wishart “Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences.” Derrick E. Fouts “Prophage Finder: A Prophage Loci Prediction Tool for Prokaryotic Genome Sequences.” M. Bose and Robert D. Barber “Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes.” Samuel Karlin “Searching for a ''Hidden'' Prophage in a Marine Bacterium.” Yanlin Zhao, Kui Wang, Hans-Wolfgang Ackermann, Rolf U. Halden, Nianzhi Jiao and FengChen “Switches in Bacteriophage Lambda Development.” Amos B. Oppenheim, Oren Kobiler, Joel Stavans, Donald L. Court, and SankarAdhya

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