1. Lysogeny: Phage Entry into Bacterial Hosts Bobby Chaggar Yordanos Teferra

3. attP and attB regions attP site of L5 phage used in comparing phages and similar attB site of M. Smegmatis used in finding other att sites.

4. Search for Similar attP regions

5. Search for similar attB sites M. Segmatis: GCGGGCGTAGCTCAATGGTAGAGCCCTAG TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTC Msme-155.Msmeg-11642Msme-155.Msmeg-11642 (4764496 -> 4764566) Aliases:(tRNA-Gly”) M. Vanbaalenii: GCGGGCGTAGCTCAATGGTAGAGCCCTAG TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCA Mvan-PYR-1.Mvan-PYR-1-10996 Mvan-PYR-1.Mvan-PYR-1-10996 (4324373 -> 4324446) Aliases:(tRNA-Gly”) M. SP.JLS: GCGGGCGTAGCTCAATGGTAGAGCCCTAGTCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTC GCCCGCTCCA M-JLS.Mjls-9576 M-JLS.Mjls-9576 (3780254 -> 3780327) Aliases:(tRNA-Gly”)

6. The Search for Prophage DNA in Mycobacteria

7. Sliding Window

8. Deviations in GC content

9. Proteins to Consider Tail tape measure protein Phage major capsid protein Large-subunit terminase Integrase excisionase

11. References Gomathi, N.S.. "In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis." ScienceDirect. 31. (2007): 82-91. Web. Hatful, Graham. "Characterization of the Mycobacteriophage L5 Attachment Site, attp." JMB. 266. (1997): 76-92. Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brussow, H. (2003). Prophage genomics. Microbiol Mol Biol Rev. 2003 June; 67(2): 238–276. doi: 10.1128/MMBR.67.2.238-276.2003 Hendrix, R., Smith, M., Burns, R., Ford, M., & Hatfull, G. (1999). Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci U S A. 1999 March 2; 96(5): 2192–2197. Evolution. Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. TRENDS in Microbiology Vol.9 No.7 July 2001