Title: Annotation of Phage Elesar

Date: 30 January 2019

Rationale: The purpose of this lab is to finish the sample annotation of gene 1 of Elesar and begin annotating other genes in order to refine the skills needed to annotate NapoleonB

Tools:

• Microsoft Surface Pro 5 Tablet
• DNA Master Software
• NCBI BLASTp Feature
• GeneMark

Procedure:

• Started DNA Master
• Performed the following sequence of commands (using a .fasta file for phage Elesar): “Export” –> “Create New Sequence from This Entry Only” –> “Genome” –> “Auto-Annotate”
•  Genes 16 and 17 were selected through the main listing of predicted genes menu, and then the “Products” tab was selected.
• Their sequences (individually) were loaded into the BLASTp feature on the NCBI website and the BLAST results analyzed in order to determine function
• The following list of commands was utilized in order to analyze the ORFs and RBS (ribosome binding sites) for each gene: “DNA” –> “Frames” –> “RBS” AND “ORF”
• Using the acquired information, the two genes were annotated

Results/Observations:

• The following annotations were made for Elesar gene 16 (along with NCBI BLASTp results):
  • SSC: 10058, 10219 CP: yes SCS: both BLAST-Start: Arthrobacter sp. yr096, q1:s1, 83%, 5 e-12 Gap: 88 LO: yes RBS: Kibler 7, Karlin Medium, 3.077, -2.367, yes
  • 
• The following annotations were made for Elesar gene 17 (along with NCBI BLASTp results):
  • SSC: 10249, 10587 CP: no, longest ORF SCS: both BLAST-Start: Arthrobacter sp. TMN-18, q1:s3, 97%, 2 e-35 Gap: 29 LO: yes RBS: Kibler 7, Karlin Medium, 2.441, -3.779, no
  • 

Conclusions/Next Steps: The next steps for this lab would be to continue annotating more genes on Elesar for practice and begin transitioning to NapoleonB. It is important too to pay close attention to the ORFs and coding potentials for each gene as the RBS seems to be the toughest to determine. Coding potential can cause ambiguity and uncertainty when annotating a gene, especially when an overlap can be observed.