Rationale: Start brainstorming ideas for different bioinformatics projects

Process:

• Looked through different bioinformatic software and find topics of interest
• Designed 4 different research questions

Results:

Questions:

1. Are there repeats in NapoleonB? Are these segments specific to NapoleonB or found in other phage? Can we find meaning in this information (we hope so)?
2. Are there sections of NapolonB’s genome that have significantly different %GC composition than the genome as a whole? Do these parts match other phage or bacteria (new acquisitions?)? How common is this for Arthrobacter phage?
3. How conserved are phage genes? What genes do NapoleonB and most other AM cluster phage have in common? What about all Arthrobacter phage? How similar are the DNA sequences?
4. Does NapoleonB have any Rho terminators and can we use protein folding software to predict their structure? Are these structures common in other Rho terminators for Arthrobacter phage?

Lathan liked question 3 so we did some refining:

• To refine maybe find several conserved genes for each cluster (or a couple clusters) and compare these
• Also look for areas within clusters where genomes vary significantly
• Does genome length effect similarity
• Will phamerator allow us to compare cross cluster
  • Rachel says we can edit the code so that we can do this
• We can also look and see if any of the known function gene hits didn’t hit to an AM cluster or had other good hits to phage outside the cluster

Next Steps:
Get question approved my Leo and develop research methods