Rationale:

The purpose of the lab was to annotate the remainder of NapoleonB’s genes with the knowledge and skills acquired in the past few weeks.  

Tools: 

• DNA Master 
• PhagesDB  
• NCBI BLAST 
• Phamerator 
• HHPred 
• GeneMark  
• PhageNotes 

Procedure: 

1.  FASTA file of NapoleonB was opened on DNA Master.  
2. Genes were located and protein sequences were used in PhagesDB, NCBI BLAST and HHPRED.  
3. Phamerator, and GeneMark were used for Synteny and  Coding Potential. 
4. Annotations of gene 14,15,16 and 96 were completed and saved on PhageNotes.

Results: 

Annotations of Gene 13,14,15,16, and 96 

ORF’s for genes:

Conclusion: 

Gene 13, and 15 had no function, but genes 14,16,96 had a function.  Gene 14 and 16 were major tail proteins supported by NCBI BLAST, PhagesDB, HHPred, and Phamerator.  It was difficult to determine the start of gene 96 since there was a huge gap between gene 96 and 95. Also there was a slightly large overlap between gene 96 and 97. GeneMark was used to view the coding potential and the results showed that there was no significant coding potential, so the start was not changed. HHPRED produced different results and suggested that gene 96 was a VVR-NUC domain, while NCBI and PhagesDB suggested that gene 96 was a hydrolase.

Future Work:  

The Annotated genes will be reviewed for correctness, and annotations may be changed if needed. After all the genes have been annotated, NapoleonB’s data will be used to test a scientific question.