Annotation Practice and Elesar Phage Notes 2/6/2019

Rationale

The rationale behind these procedures is to learn how to add annotations to phage notes and how to use phamerator and starterator.

Tools/Procedure

1. DNA Master was opened and the previous Elsar file was loaded
2. Learned how to use phamerator
3. Previous annotations were checked and added to phage notes
4. Phages DB was used to compare gene start calls to starterator results

Results

Gene 10 – SSC:7514 – 7813, CP:No Didn’t want overlap, SCS:Both, ST:NI, BLAST-Start:No significant NCBI BLAST alignments, No significant PhagesDB BLAST alignments, Gap:2bp gap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.299 -4.08 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF

Gene 11 – SSC:7829 – 8230, CP:No no start codon avaiable to cover the coding potential, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage Ryan gpNA NCBI BLAST q1:s1 0.95 2E-70, Aligns with Phage Ryan gp12 PhagesDB BLAST q1:s1 0.96 2E-67, Gap:15bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 2.565 -3.515 No, F:head-to-tail adapter, SIF-BLAST:head-to-tail adapter Supported by NCBI BLAST Phage Ryan gp12 AYN59006.1 0.95 2E-70, head-to-tail adapter Supported by PhagesDB BLAST Ryan gp12 MH834627 0.96 2E-67, , SIF-HHPred:NKF, SIF-Syn:head-to-tail adapter, upstream gene is NFK, downstream gene is Head-to-tail stopper, just like in phage Ryan

Conclusion

These results are very similar to the results of last lab with the exception of the starterator information. The results further support that gene 11 is a head-to-tail adapter and that gene 10 is an orpham that codes for a hypothetical protein not common in other sequenced DNA. Because this was just a learning experience not much else can be concluded from these results.

Future Plans

In the future, I will use what I learned how to do in this procedure when I am analyzing the genome from Napoleon B. Annotating in phage notes will be extremely helpful because they give me correctly formatted annotations that can be copied into DNA master to prevent any mistakes. I will also begin to use tools such as starerator when making calls about genes from Napoleon B.