Rationale:

The purpose of today’s lab was to go over genes that were marked as red flags and to justify the annotations or fix them.

Tools:

• DNA Master
• NCBI BLASTp
• PhagesDB BLAST

Procedure:

• Gene 64 raised questions regarding the open reading frame selected for the start.
• Once I was assigned the gene, I looked into it to try and justify the selected call.

Results:

• Original Glimmer call @bp 35903 has strength 11.27
  SSC:35903 – 36703, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage KeaneyLin gp58 NCBI BLAST q1:s1 0.99 0, Aligns with Arthrobacter Phage KeaneyLin gp58 PhagesDB BLAST q1:s1 1 e-155, Gap:4bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.007 -3.956 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF
• 

Conclusions:

It was decided to keep the gene were it was originally called as pulling the gene further back would have violated the guiding principle of phage annotation by creating too large of an overlap in the phage genome. Although it is not the longest open reading frame, it is as far back as possible without violating the guiding principle.

Next Steps:

The next steps are to continue checking final gene annotations of NapoleonB and review abstract submissions for Scholar’s Week.