Date of Lab: 01/31/17

Rationale: The purpose of the lab was to practice genome annotation and learn how to use Phamerator.

Tools used: DNA master, NCBI, Phamerator

Procedures:

1. Open the software Phamerator through virtual box and login with the password “phamerator”.
2. Under “Phages” tab> search the interested gene (It will allow you to look at multiply genes at the same time) > MAP
   1. the number in the colored box = gene number
   2. number above the box = pham number
   3. number in (#) = number of members in that pham
   4. lines on the graph: identifying sequence that are similar on other part/ duplication/different place/ phage
   5. upper gene= forward
   6. lower gene = reverse
3. If we pointed at the gene/the rectangle, it would show the function of the gene(only apply on some genes)
4. Annotate the assigned gene (gene 22)

Conclusion:

We got to learn to use a new tool to help us to annotate the genes with more details and have more practice on annotating the genes.

Notes:

• each ruler = genome
• rectangle = auto annotated gene
• high gene density
  • shouldn’t have too many gap/overlap–should be packed
• there will be gap for promoter between genes
• If it is a perfect match :
  • query coverage ~200%
  • E value ~ 0
• Long DNA = tap measure gene
• Short gene = regulator
• F = function
• Fs = function source: blast, pharmarater, HHpred, cdd(conserved domine), record best blast