02/13/19

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 72 was annotated
7. NCBI was used to blast the 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 the gene and the possible changes that could be made if possible to acquire the longest ORF possible.
9. Phagesdb was used to blast the 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

NCBI ,BLAST and HHpred yielded the above results for gene 72.

Conclusion:

Gene 72 has no known function because the Blast matches are hypothetical proteins and HHpred yielded a hypothetical protein.

Future Steps

Don’t really know what we are going to do now. most likely begin discussing results of the annotation.

Annotation of NapoleonB 2/11/2019

Rationale

The rationale behind these procedures is to start annotations on NapoleonB so that other research can be conducted.

Tools/Procedure

1. NapoleonB FASTA file was downloaded
2. FASTA file was opened (File > Open> FastA Multiple Sequence File)
3. Contents of the file were exported (Export . Create Sequence from this Entry Only)
4. Contents of the file were auto annotated (Genome > Auto Annotate > click “yes”)
5. Reading frames were examined (Genome > Frames> click “ORFS” button)
6. Gene locations were compared paying attention to gaps and overlap
7. NCBI, Phages DB, and HHPred systems were used to BLAST amino acid sequences
8. Starterator and genemark were used to determine if the genes ought to be altered to include more or fewer base pairs
9. The information gathered was used to update phage notes

Results

Gene 65- SSC:41757 – 41909, CP:Yes, SCS:Glimmer, ST:SA, BLAST-Start:Aligns with Arthrobacter phage Cheesy gp63 NCBI BLAST q1:s1 0.87 7E-22, Aligns with Arthrobacter Phage Cheesy gp63 PhagesDB BLAST q1:s1 1 7E-20, Gap:24bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 3.269 -2.511 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:, upstream gene is , downstream gene is , just like in phage

Gene 66- SSC:41909 – 42091, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage Cheesy gp64 NCBI BLAST q1:s1 0.86 2E-24, Aligns with Arthrobacter Phage Kardesai gp65 PhagesDB BLAST q1:s1 1 4E-27, Gap:1bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium , F:NKF, SIF-BLAST: Supported by NCBI BLAST gp , Supported by PhagesDB BLAST gp , supported by a CD found from the databse gp , , SIF-HHPred: supported by gp , SIF-Syn:, upstream gene is , downstream gene is , just like in phage

Conclusion

There is very little information from which to draw conclusions about the data set; however, it appears that there is no known function for genes 65 and 66. As the rest of Napoleon B is annotated I will be able to draw more conclusions from the data.

Future Plans

In the future, I will continue my annotations of NapoleonB with the goal of being able to research my own questions once the gene is fully annotated.