Kirsty Wyatt

Lab Date: 2/28/17

Purpose: This lab assigned us and gave us time to annotate about five genes from Timinator.

Methods:

Open DNAMaster, Starterator, Phamerator, PhagesDB, NCBI, HHPred

Annotate genes accordingly, refer to earlier lab notebook posts

Insert results into the google document accordingly

Conclusion:

This lab gave us a chance to practice annotating genes on our own multiple times. There were plenty of challenges when doing this individually, but gave us a great opportunity to learn.

Future work: Begin brainstorming for research projects

Kirsty Wyatt

Lab Date: 4/12/17

Purpose: This lab was to continue our research and further our understanding of our topic.

Methods:

Review work from previous lab

Finish annotating genomes

Run through Phamerator with Timinator

Compare and add

Conclusion:

When putting through Phamerator, we found that most of the genomes shared gene 27 as their holin gene. This gave us hope that we were headed in a direction.

Future Work: send sequences to RaptorX, compare results, continue adding to components of poster

Kirsty Wyatt
Lab Date: 03/14/17
Purpose: This lab was to begin brainstorming research poster project ideas/topics.
Methods:
Complete Timinator gene annotations
Look up published articles to find possible research topics
Work with group to begin thinking about a topic
Refer to uploaded powerpoints on Canvas to begin thinking about what is needed for a research poster
Conclusion:
Kiersten S., Theresa W., and I make up my group. This lab is teaching us how to work as a team when coming up with ideas. We are leaning towards the holing gene.

Future work: Begin/finish annotating Timinator, begin annotating other genes from same Pham

Kirsty Wyatt
Lab Date: 2/23/17
Purpose: We took lab time to present and discuss annotations made on Lore genes and to work as a team to help finalize the annotations.
Procedure:
1. Submit PowerPoint presentation
2. Present
3. Discuss why the annotations were made and if there are any concerns
4. Gene 13 needed no changes, it also agreed with another group’s annotations on the same gene
5. Preparation to submit all the annotations for publication
6. Review over annotations, put them into one container (excel, googledocs, Word, etc), BLAST them all again, compare the new BLASTS with the older, make changes if necessary, collect all names of the authors, collect ideas for a cover page, create a cover page, submit.
Conclusion: This lab was interesting because we got to observe, analyze, change, discuss everyone’s annotations and why they annotated it that way. As a group, we learned together. It is exciting to be published on something that is currently a hot topic for scientists.

Kirsty Wyatt
Lab Date: 2/19/17
Purpose: This lab is to aid us on how to recognize and fix any common mistakes that are possible to occur when annotating a gene. We were encouraged to relook over our annotated gene from last lab.
Procedure:
1. Open DNAMaster, GeneMark, Glimmer, Startertor, Phamerator, HHPred, Phagesdb, NCBI, and the googledoc containing annotation information
2. Determine a start site by comparing many of the sites listed above
3. Refer to the Shine Delgarno to ensure the start site chosen will not cause too big of a gap/overlap
4. Look at the reading frames and choose the longest
5. Identify any possible functions using and comparing many of the sites listed above
Conclusion:
A few mistakes were made, but they were identified and fixed. Looking over our annotations was helpful because we carefully analyzed our work, thus gaining a better understanding of it. We didn’t choose the best score for SD because it would go against starterator and it would have created too large of a gap.

Kirsty Wyatt
Lab Date: 02/08/17
Purpose: This lab was to familiarize ourselves with Starterator and its usefulness in annotating genes.
Procedure:
1. Open virtual box
2. Open Phamerator
3. Update Phamerator
4. Search for your gene, and 4-6 others to compare
5. Observe the results
6. Take note of Pham number, members of the Pham, and the cluster within the Pham
7. Close Phamerator
8. Open Starterator
9. Compare the start sites on Starterator with those on GeneMark, Glimmer, DNAMaster
10. Note if you changed your starting site
11. Finish annotation
Conclusion:
In this lab, I annotated gene 13 from Lore phage with a partner. Together, we used all the sites and formulated a complete annotation. I got more practice with annotations and using the different sites and how they all compare and correlate.

Kirsty Wyatt
Lab Date: 2/1/17
Purpose: This lab was to familiarize ourselves with Phamerator and its usefulness in annotating genes.
Procedure:
1. Open virtual box
2. Open Sea2017
3. Open Phamerator
4. Update Phamerator
5. Search for your specific genome and 4-6 more to compare
6. Observe the results
7. Take note of Pham number, members of the Pham, and the cluster within the Pham
8. Identify the function of gene if it is included
9. Begin another annotation in DNAMaster, now including information derived from Phamerator
10. You can now fill in BLAST, F: (top hits), and FS: (sources used)
Conclusion: Phamerator is an interesting tool with a colorful layout. It is almost unbelievable how many different sources are available for gene annotating. The more practice, the better, and I feel much more knowledgeable about annotating a gene.