Title: Independent Research

Date: 27 March 2019

Rationale: The four previous research topics will be reconsidered and one topic will be selected as the final project

Tools: 

• DNA Master
• Gepard
• NCBI BLASTn

Procedure: After discussing as a group, the decided upon topic was repeat sequences in NapoleonB’s genome. Therefore, Gepard and DNA Master were used to locate sequences of interest that repeated throughout NapoleonB’s genome. Once a potential repeated sequence was identified, it was entered into DNA Master’s “Scan” feature to check if it repeated a significant number of times. Potential repeat sequences were also BLAST’ed by NCBI’s BLAST database to see if they appeared in other phage genomes.

Results/Observations: One 51-base pair sequence was shown to repeat twice in NapoleonB’s genome, as well as show BLAST results for many other AM cluster phages. No other found repeat sequences showed significance.

Conclusions/Next Steps: Gepard will be used continuously throughout the experiment in order to locate sequences of interest. The specific location of the repeat will also give clues as to why the repeat exists. The main point of the project is to investigate whether or not a repeat sequence can be used as a “tag” in order to reverse an “NKF” call made on the annotation of NapleonB.