02/11/19

Rationale:

to acquire the annotated genome of  napoleon b,

Procedure:

1. opened  DNA master
2. Opened FastA file for napoleon b using the following steps, File>open>FastA multiple sequence file> Choose NapoleonB.FastA
3. clicked export on window with the extracted file and then choose Create sequence from this entry only.
4. opened frames and went to DNA> Frames.
5. then clicked ORF on the new window to see the highlighted genes.
6. Gene 69, 70, and 71 were annotated
7. NCBI was used to blast each gene and acquire genes in the database that matched with the query gene, which was used to find the possible similarity and function of the query gene
8. Genemark was used to check the coding potential covered by each gene and the possible changes that could be made if possible to acquire the longest ORF possible.
9. Phagesdb was used to blast each gene and acquire genes in the database that belonged to other phages that matched with the query gene, which was used to find the possible similarity and function of the query gene
10. HHpred was used to predict the protein structure of the gene product, which was run through its database (Pfam and COG)for a possible matches with other proteins, which could be used to predict the function of the protein.
11. Phamerator was used to compare the genome of napoleonb to other phages in the same category to compare syntony of the genes.
12. phage notes was used for input of all the required information for genomic annotation.

Results:

the function declared for all three genes was “no known function”.

the BLAST results yielded genes of unknown function, same was concluded for HHpred.

Conclusion

these three genes have no known function and do not seem to have any significance as of now. nothing further can currently be concluded.

Future steps

Finish annotation by annotating gene 72.