Name: Micah Heimbuch

Date: 18 April 2017

Purpose: The objective of this lab was to finish our poster.

Methods:

1.      Finish template

Conclusion:

Hope finished the template, Will wrote the abstract and I finished the intro and the bibliography.

Name: Micah Heimbuch

Date: 11 April 2017

Purpose: The Objective of this lab was to finish the rough draft of the research project.

Methods:

1.      Finish Poster

2.      Analyze Results

3.      Type Intro

4.      Read more outside research

Conclusions:

We discovered that the phages with large pecent differentials still had relatively similar structures. They all have a similar horse shoe appearance and clusters of alpha helix foldings. I still need to do more research on the actual function of TMP and figure out if the similar structures have any significance or if it was just by chance.

Name: Micah Heimbuch

Date: 28 March 2017

Purpose: The objective of this lab was to further develop our project.

Methods:

1.      We looked at example posters to help with formatting

2.      We submitted the tape measure protein genes into Raptor X

Conclusion:

Our refined question is “What is relationship between the different protein sequences of tape measure proteins in bacteriophages and their structures?”  Our hypothesis is that Tape measure proteins have similar function in all phages, therefore; they will have similar structure as well. We learned what the Swiss model really is and I personally don’t believe the data will be useful to our study. We submitted genes to Raptor X and are now waiting for those results to come in.  We will later compare the predicted structure of the genes to each other with relation to their percent similarities in their gene code.

Name: Micah Heimbuch

Date: 21 March 2017

Purpose: The objective of the lab was to continue forming a hypothesis for research.

Methods:

1.      Research the differences between the Swiss Model and Raptor X

2.      Talked to Lathan for ideas and looked at posters from previous years

Conclusions:  We began by looking at the Tape measure protein and discussing its similar role in almost all phages. Tape measure protein has the same basic function even when its in different phams. This lead us to ask the question “Will tape measure proteins with different phams, despite their percentage difference within nucleotide sequence, still produce similar structures?”  In order to compare the sequences of DNA we ran three different tape measure proteins from different phams through NCBI. We then ran them through the Swiss Model which gave back weird results that we didn’t fully understand. The next step will be to send in the proteins to Raptor X and better understand the results from the Swiss Model.

Name: Micah Heimbuch

Date: 14 March 2017

Objective: The purpose of this lab was to begin to form potential hypotheses.

Methods:

1.      Finish Annotations

2.      Form group and brainstorm different questions about phages.

3.      We looked at RaptorX, Swiss Model, NCBI, and Phagesdb

I am in a group with Will and Hope.  We looked at the tape measure protein and the HTH binding proteins, holing and lysine. We think we are going to look at the structure of tape measure proteins but we do not have a full hypothesis yet.

Name: Micah Heimbuch

Date: 28 February 2017

Purpose: The objective of this lab was to annotate the genes we were each given in Timinator.

Methods: We downloaded the Timinator.fasta file then annotated the genome using DNA master, NCBI, Phagesdb, HHpred, and a google document which the whole class uploaded their phages to a google doc.

Conclusions: I annotated genes 7, 29, 51, 73, 44. All of these genes did not need to be corrected and all were auto annotated. None of the genes had a known function.

Lab 7

Name: Micah Heimbuch  

Date: Tuesday, February 21, 2017

Objective: The objective of this lab was to check all annotated genes from Lore before sending the annotated genome to NCBI

Procedure:

1.      Finish powerpoint and genes annotated

2.      Present in front of class and provide evidence for why we called starts where we did

Conclusion: Discussing each gene was very helpful and many mistakes were corrected. Genes 3, 16 and 21 were interesting and notes were taken for each. Gene 3 might have a longer start then originally called. Gene 16, my gene, had a query of 3 and subject of 2. Gene 21 was deleted and might be a reverse gene on a different ORF.

Lab 6

Absent

Lab 5

Name: Micah Heimbuch

Date: Tuesday, February 7, 2017

Objective: The objective of the lab is to annotate an unknown gene on the Lore genome and learn how to use starterator.

Procedure:

1.      Open DNA master and auto annotate genome

2.      Annotate assigned gene and plug data into new google drive instead of DNA Master

3.      Attempt to Determine Function of Gene

Conclusion: I was able to work on and finish gene 16. The query was a 3 and the subject was a 2 however there was no other good start to use which was interesting. Starterator was helpful for providing more evidence to back my start choice.

Lab 4

Name: Micah Heimbuch

Date:  Tuesday, January 31, 2017

Objections: The objective of the lab was to use phamerator to discover the function of genes. After we learned how to use phamerator we annotated a gene using tools such as HHPred and the Conserved Domain Database.

Procedures:

1. Open Virtual Box and select phamerator.

2. Select the Link Phage as well as six other genomes.

3. Select Map then complete questions that matter.

4.  Annotate assigned gene. Find the  “SCS: CP: SD: SCS: Gap: Blast: LO: ST: F: FS:”

5. Find Function of Gene using NCBI, CDD and PhagesDB

Conclusion: Phamerator uses genomics(honestly no idea what this is) using sequence alignments in order to narrow databases and lets us view different drafts