Rationale:

To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. Phage Elesar was picked to be the sequence for the tutorial, in order to familiarize with the functions and features of the software.

Materials:

• Laptop
• DNA Mastering Program
• Gene sequence of phage Elesar

Procedure:

Used the protein sequence of gene 23 and 60 in phage Elesar and search for protein structure or conserved domain hits on HHPRED to determine possible functions for the annotated proteins:

Protein sequence for gene 23:

Protein sequence for gene 60:

The probabilities and E-values were considered for the hits:

gene 23:

gene 60:

The hits were abandoned due to the E-value exceeding 10^-4 and the probability being under 90%, respectively.

The results along with the notes taken last week were corrected and submitted on an online spread sheet.

Results/Next Steps:

gene 23:

SSC: 17875, 18093 CP: yes SCS: Glimmer ST: BLAST-Start: Arthrobacter phage Maja, PBI_MAJA_20, NCBI, Q1:S1, 98%, 7e-39 Gap: overlap 195 LO: yes RBS: Kibler7, Karlin Medium, 2.822, -2.892, no F: NKF SIF-BLAST: NKF SIF-HHPred: NKF

gene 60:
SSC: 39077, 39397 CP: yes SCS: Both ST: BLAST-Start: Arthrobacter phage Ryan, PBI_RYAN_63, NCBI, Q1:S1, 93%, 2e-60 Gap: 2 LO: yes RBS: Kibler7, Karlin Medium, 2.150, -4.606, yes F: NKF SIF-BLAST: NKF SIF-HHPred: NKF

The gene functions are unknown, although matching with phages Maja and Ryan, the sequence was projected as hypothetical proteins.

In the next Lab, SIF-Syn and PhageNotes would be explained.