Problem Sets

1. Questions and Key
2. Questions and Key
3. Questions and Key

Supplementary Instructions

1. Basic Instructions for Sequence Improvement
2. How to Design Oligos (Primers)
3. How to Export the Consensus Sequence

Literature

Mullis, Kary B (April 1990)  The Unusual Origin of the Polymerase Chain Reaction.  Scientific American 262: 56-65  (RR)

Crick, FHC (1966)  The Genetic Code: III.  Scientific American 215: 55-62   (RR)

Eddy, Sean R (2004)  What is a hidden Markov model? Nature Biotech 22: 1315-16.

Webber, C and Ponting, C P (2004)  Genes and homology.  Curr Biol 14: R332-3.

Hatfull, GF, and GJ Sarkis (1993) DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Molec. Microbio. 7: 395-405.

Pedulla, M et al (2003)  Origins of highly mosaic mycobacteriophage genomes.  Cell 113: 171-182 (tentative).

Hatfull, GF, ML Pedulla, D Jacobs-Sera, PM Cichon, A Foley, ME Ford, RM Gonda, JM Houtz, AJ Hryckowian, VA Kelshner, S Namburi, KV Pajcini, MG Popovich, DT Schleicher, BZ Simanek, AL Smith, GM Zdanowicz, V Kumar, CL Peebles, WR Jacobs Jr, JG Lawrence, RW Hendrix (2006). Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS 2: e92.

Hatfull, GF, SG Cresawn, RW Hendrix (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution.  Res. Microbiol. 159: 332-339.  (RR)

Faruque, SM, MJ Islam, QS Ahmad, ASG Faruque, DA Sack, GB Nair, JJ Mekalanos (2005)  Self-limiting nature of seasonal cholera epidemics: Role of host-mediated amplification of phage.  Proc Natl Acad Sci  USA 102: 6119-6124.

Websites

• Introduction to Protein Structure