03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. Coaches were consulted for the validity of each questions and for approval of question
2. Group researched and compiled more information on the topic of Start site preferences,
3. After some misconceptions were cleared, a question based on start site preferences was refined and approved by the coach
4. the group decided to look into the start site preferences of genes in different genomes of arthrobacter phages of CLuster AM and other phage clusters. after hard data is compiled on the start site preferences, the group will derive conclusions based on the acquired data.
5. the group will then use modeling software to see how different start sites will affect the structure of the protein produced by the gene. these will be the theoretical results.
6. possible tools that can be used were compiled.

Results

the research question for individual research

1. What are similarities and differences in the start codons for the nucleotide sequences coding for tape measure, major and minor tail proteins? is there a prefered start codon based on the cluster? How is the structure of the produced protein affected if a different start codon is used?

Tools: NCBI. PhagesDB, HHpred, SWISS Model Workspace, Openstructure and SWISS Pdb viewer.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. it may answer some questions about the phage genomes and possibly provide another attribute that can be used for gene annotation.

Future steps

do more research, look into primary literature and find more tools that can be used.