DNA in mycobacterial genomes Bobby Chaggar BNFO 301 Lysogeny Group Compare SEQUENCESIMILARTO each lysogenic mycobacteriophage to a list of all mycobacteria in BioBIKE PhAnToMe ID: 931548
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Slide1
Identifying probable prophage DNA in mycobacterial genomes
Bobby Chaggar
BNFO 301
Lysogeny
Group
Slide2Compare (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
Experimental Design
Slide3Example: Comparison of Mycobacterium-phage-Tweety43.6% ID (e-value = 8.00e-100) with Mycobacterium-Marinum-
M’s p
3540Outranked 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
Result
Slide4Ex. Sequence similarity with mycobacterium marinium M.
Slide5“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 Feng Chen“Switches in Bacteriophage Lambda Development.” Amos B. Oppenheim, Oren Kobiler, Joel Stavans, Donald L. Court, and Sankar Adhya
References