NapoleonB Genes 26-28 (2/13/19)
Rationale:
Annotate NapoleonB genes 26-28 to complete the section of genes assigned. Once NapoleonB genome is fully annotated, ideas for what research question should be investigated with this data can be explored.
Tools:
- DNA Master
- NCBI
- PhagesDB
- GeneMark
- HHpred
- Phamerator
- phage notes
Procedure:
- Conducted a GeneMark on NapoleonB.
- Determined the stop and start with the highest coding potential for genes 26-28 based off the “Choose ORF Start” window and the GeneMark.
- Performed a HHpred search on NapoleonB genes 26-28.
- BLAST was performed on NapoleonB genes 26-28 through both NCBI and PhagesDB.
- Annotated NapoleonB genes 26-28.
Results:
The following image shows NapoleonB gene 26-28’s annotations.
The following images show the BLAST E-values for gene 26 from the start codon which Glimmer and GenemMark called.
The following images show the BLAST E-values for gene 26 from the new start codon which has the longest reading frame.
Conclusion:
On gene 26, it was determined that the start codon should be moved from what Glimmer and GeneMark called (bp 24817) to an earlier start codon (bp 24802) because the BLAST E-values were smaller, more coding potential would be covered, and this would make the gene have the longest open reading frame. Genes 26-28 had no known function.
Future Work:
NapoleonB’s annotations will be checked and research questions to be investigated will be brainstormed.
