Annotation of Phage Elesar Gene 1

Date: 1-28-19

• Rational
  • The rational for this lab was to annotate the first gene in phage Elesar in order to gain practice in annotation before transitioning to phage NapoleonB.
• Procedure
  1. DNA Master was opened.
  2. Export > Create New Sequence from This Entry Only > Genome > Auto-Annotate was used to auto-annotate the phage genome.
  3.  Gene 1 was selected through the listing of predicted genes, and the Product (the results of the amino acids coded for) were copied.
  4. The amino acid sequence was loaded into the BLASTp feature on the NCBI website and the BLAST results were analyzed and recorded on the template.
  5. Ctrl + Alt + F brought up the Frames of the genome, ORFS was selected to show the locate open reading frames, and RBS was selected to determine the ribosome binding site for the first gene
  6. Using the acquired information, the first gene was annotated.
• Results
  • The following annotations were made for Elesar gene 1 :
    • SSC: 45, 353
      • The start location was moved from bp 84 to bp 45 to achieve the longest open reading frame.
    • CP: yes
      • GeneMark was used to compare the coding potential to the annotation. The selected species was “Arthrobacter_aurescens_TC1” and the results were as follows:
      • 
    • SCS: both-cs
      • DNAMaster reported “Original Glimmer call @bp 84 has strength 8.51,” so both Glimmer and GeneMark called the gene at bp 84, but the starting base pair was instead decided to be bp 45.
    • BLAST-Start: no significant BLAST alignments
      • The e value for the BLAST of gene 1 returned as 1.11, outside of the range of accurate matches.
    • Gap: first gene
    • LO: yes
    • RBS: Kibler7, Karlin Medium, 1.222, -6.751, no
      • The total score was not the best for this RBS, but it was decided that this was still the best location for it.
• Conclusion
  • It is important to declare which database (NCBI or PhagesDB) is being used, as each BLAST can return different results depending on the database.
• Future Plans
  • The next step is to continue annotating more genes on Elesar for practice before transitioning to NapoleonB.