Rationale:

The purpose of today’s lab was to move through the genome as a class to catch any last mistakes before Leo and Lathan comb through the genome before submitting.

Tools:

• DNA Master
• NCBI BLASTp

Procedure:

• As a class, the lab reviewed any gene that raised any red flags while scrolling through the annotation.
• Gene 61 raised a red flag regarding the selected start as there was one longer open reading frame that could have been selected.
• Re-checked and fixed the initial gene annotation on 61.

Results:

• Original Glimmer call @bp 36690 has strength 7.46; GeneMark calls start at 36693
  SSC:36690 – 37253, CP:Yes, SCS:BothGL, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Mudcat gp57 NCBI BLAST q2:s1 0.99 3E-17, Aligns with Mudcat gp57 PhagesDB BLAST q2:s1 0.99 1E-108, Gap:14bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 3.118 -2.454 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF
• 
• Blast Results
  • 

Conclusions:

It was decided to pull the gene back to the start at 36690 base pairs. This correction was decided as pulling the gene back resulted in a better query coverage with the BLASTp hit as a q1:s1 instead of a q1:s16 that the other start yielded.

Next Steps:

The next steps for this experiment are to finalize the gene calls for NapoleonB and submit a final abstract for Scholar’s Week.