What Went Well:

The intro and the cooperation amongst each of the group members allowed us to have a fluid presentation, we were well versed in our phage research.

What Went Roughly:

There were some initial hick-ups with the presentation. The first dilemma was the timing, we had to start 15 minutes earlier than we thought we would and a crucial member of the team was missing so I had to cover for her. The second hick-up was that the professor was much more versed in phage therapy than I was so I had little to no buffer with our poster being “something fresh” for him. Of course he asked some questions that I wasn’t prepared for, only because they were a stretch for the amount of understanding we had in the actual DNA sequencing process.

Yet Overall I think he was interested in our presentation and we ended up having a greater appreciation for all the work we accomplished.

Goal/Rationale:

Today Noah and I will again use the Single gene sequencing tool to evaluate the conservation of genes within the clusters. Through this program we will be able to quantify Andreas Gepard-dotplot data, and get a clearer picture of how conserved the selected genes are to each other.

Tools/Procedure:

We will once again be using phagesDB and the Single Gene sequencing tool to analyze how similar the same genes are across phages of different clusters as well as within the same cluster. High percentages for similarity from the genes within indicate a low degree of conservation. A high percentage of similarities between genes that come phages of different clusters would indicate that it would be a less effective tool for single gene analysis.

Results:

(Taken from the Single Gene sequencing tool)

Terminase Large Subunit-

Portal Protein-

Capsid Maturation Protease-

TMP-

Conclusion:

We found that the TMP gene was less actually less conserved than the other genes we compared it to, showing that while the TMP gene is very capable of single gene identification (as seen from the literature), the findings of our method indicates that other .

What To Work On:

The next step will be for Noah and I to come together to formulate a power point with a generalized form of our data as well as the data from Andreas Gepard-dotplot.

Goal:

To present our findings to the class and receive constructive criticism for improvement.

Results/How it went:

We were somewhat unprepared for the presentation, but we learned what needs to be improved. Our introduction needs work as it doesn’t adequately describe the “so what”, of our presentation. The data needs to inserted in a more understandable format, so adding another chart that summarized all the data on the differences between phages compared from different clusters would help.

We simply prepared for the upcoming scholars week, not much can be elaborated on.

We presented our poster to class today and I must admit that I need to practice for the presentation on Friday. It wasn’t so much as a failure to understand the work we had done but rather a… performance issue that I will remedy. But besides from that I think my group came together with a very well prepared poster that I hope will be chosen for the official presentations.

In Lab we had a very productive session with having the intro finished as well as creating a firm grasp on what each of us should do for the remaining sections of the poster. It has been a challenge to avoid blocky boxes of text in the presentation.

Today in class I worked with my assigned group on how we would want to arrange the poster. We ended class with most of us feeling very good with a horizontal oriented methods section. I will revise my work on the Introduction in the next lab.

Name: Jake Hanna

Goal:

To finish annotating gene 9 and onward until completion.

Tools: 

DNA Master, Starterator, Phamerator, phagesDB blast, HHPred Blast, NCBI Blast, Gap

Results:

Gene 9:

Blast:

PhagesDB- good hit

NCBI- good hit

HHPred- No Hit

Gene 10:

S.D.:

Coding Potential:

Blast:

PhageDB- good hit

NCBI- good hit

HHPred- good hit

Gene 11

Coding Potential:

S.D.:

The initial Z-score is very low and the best z-score results in a gene with less than 200 bps so I will compare the two blast scores.

Blast:

PhagesDB- good hit

NCBI- good hit

HHPred- No hit

BLast for Gene 11_2

PhagesDB- poor hit (Q1:S8)

Decision:

Because the Blast hits for 11_2 were poor and all other starts other than the original would result in less than 200 bps, the original call is the most viable option.

Name: Jake Hanna

Goal:

Seeing as I somehow managed to finish annotating all my genes with time to spare, I volunteered to annotate gene 67 of Caterpillar.

Tools: 

DNA Master, Starterator, Phamerator, phagesDB blast, HHPred Blast, NCBI Blast, Gap

Results:

GENE 67

Coding Potential:

Genemark showed no coding potential.

Blast:

PhagesDB- no hit other than itself

NCBI-no good hit

HHPred-no good hit

Z-Score:

poor (Z<2)

Seeing how a better z-score could be attained with shrinking the gene from the start of 45537 to 45782, I decided to test it out.

GENE 67_1

Coding Potential:

No C.P. with Genemark as before

Blast:

PhagesDB- no good hit

NCBI- no hits

HHPred- no good hit

Z-Score:

Since (while the Z-score had improved) no better results could be found I decided to try the next best option.

Coding Potential:

Same as before

Blast:

PhagesDB- good hit

NCBI- good hit

HHPred- No significant Hits

Z-Score:

Decision:

The start on 45682 (67_2) was the best alternative-despite being less than 200 base pairs long-because of it’s excellent blast results.

Name: Jake Hanna

Goal:

To Annotate Gene 7 and onward until completion.

Tools: 

DNA Master, Starterator, Phamerator, phagesDB blast, HHPred Blast, NCBI Blast, Gap

Results:

Gene 7

S.D:

Coding Potential:

Blast:

NCBI- good hit

Conserved Domain Hit

PhagesDB- good hit

HHPred- No Hit

Gene 8

S.D.:

Coding Potential:

Blast:

NCBI- good hit

PhagesDB- good hit

HHPred- good hit

Gene 9:

S.D.:

Coding Potential:

Goals For Next Lab:

To continue to annotate gene 9 and then keep moving forward.