Rationale: Now that I have learned how to use each Biotech tool I will begin annotating the genome of the phage I discovered the previous semester, along with the help of my classmates. I was tasked with annotating genes 29-32 and 94.

Tools: PhageNotes, DNAMaster, NCBI, PhagesDB, Phamerator, HHPred, Genemark

Procedure:

1. First loaded the FastA file of NapoleonB into DNAMaster and auto-annotated the genome.
2. Checked the Frames view in DNAMaster to see if gene 29 was marked at its LORF. Opened the Genemark file for NapoleonB and found that the gene was covering all the coding potential at that area. Noted the start and stop locations and that the coding potential was completely covered.
3. Using PhagesDB I found that the starterator for gene 29 doesn’t have enough annotated calls to get any information from.
4. I then BLASTed the product of the gene through the NCBI and PhagesDB databases. Both returned the same result as the best hit. However, the hit didn’t have any result for the function. I then ran the product through HHPred and it didn’t return any hits with a decent probability.
5. I then calculated the gap of the gene and recorded the RBS results.
6. I started working on gene 30 and using the Phamerator comparison with other phages in the same cluster, the BLAST results of the gene, and the fact that the gene is a reverse gene in the middle of a forward cassette to determine that the gene needs to be deleted.
7. Recorded all my findings in PhageNotes.

Results:

BLAST for Gene 29 and Gene 30

Conclusion and Future Work: I found that gene 29 had no known function, and  gene 30 was not really a gene. In the future I will continue working on annotating the genes assigned to me so that we can have a fully annotated genome by the end of the week.