February 21

Reviewing Annotation and Poster Review 2/20/18

Reviewing Annotation and Poster Review 2/20/18

Rationale

The rationale behind these procedures is to ensure that all annotations on NapoleonB are correct and the abstract is prepared for Scholar’s Day.

Tools/Procedure

  1. Several annotations were examed as a class to ensure correctness
  2. Genes were reexamined using:
    • NCBI was used to BLAST amino acid sequences against a large database of recorded sequences
    • Starterator and genemark were used to determine if the genes ought to be altered to include more or fewer base pairs
  3. The information gathered was used to verify the gene calls that were previously made
  4. Poster requirements were reviewed to increase understanding

Results

Upon reviewing annotations a gene between genes 66 and 67 was called. It was discovered to have NKF and I will finish it annotations by Monday lab (see image above).

Conclusion

There is not a lot of information from which to draw conclusions, but it is interesting to see that there a gene in between 66 and 67 because there was no coding potential shown on genemark.

Future Plans

In the future, I will use the annotations of NapoleonB to be able to research my own questions and hopefully add in someway to knowledge about phage.

February 21

DNA Day 10

20 February 2019 ✷ NapoleonB DNA Annotation Corrections (again)

Rationale:  NapoleonB’s genes were assigned to each student to annotate and record in order to complete the genome annotation for the phage. Annotations for several genes were called into question by the TAs and the class discussed the annotations as a class.

Procedure

  • DNA master was opened and NapoleonB was auto-annotated
  • PhageNotes was opened and each aspect of the DNA annotations for several genes was analyzed.
  • Gene 23 was moved back 6 base pairs in order to generate a better q:s match in the databases.
  • Abstracts for research performed last semester and this semester were crafted prior to lab and members of the group combined the best parts of each abstract into one strong one
  • the poster for the group was somewhat planned (i.e. what should be included).

Results

 

Conclusion

Many of the genes annotated were no known function or tail proteins, so the study of the phage is largely centered around that.

Future plans

The annotation of NapoleonB’s genome will be completed, checked, and submitted to phagesdb. The information gathered from the annotation of the genome will lead to the creation of a research question and thus further research into phage biology involving NapoleonB.

February 21

Checking NapoleonB annotations

Rationale:

Check over the annotations of NapoleonB as a class in order to identify any mistakes that were made.

Procedure:

  1. Using an already auto annotated version of NapoleonB on DNA Master gene 41-44 was confirmed to have the correct annotations.
  2. Genemark was pulled and the coding potentials were doubled check for genes 41-44.
  3. The rest of the genome was proofed as a class.

Results:

The coding potentials for genes 41, 42, and 44 were covered, but 43 were not. Nothing was changed in annotations, but the annotations were doubled checked. The rest of the genome was moderately corrected in order to fix entry errors.

Conclusions:

It can be confirmed that genes 41-44 was correct in its annotation. It can also be concluded that the annotations for the phage NapoleonB are as of now correct.

Future steps:

The next step will be to conduct an independent research project and to create a poster as a group in order to present at scholars week as a class, along with finalizing a class abstract.

February 20

2.20.18 Checking NapoleonB Annotations

Rationale:

To check the annotations of NapoleonB as a class in order to catch any mistakes that were made.

Procedure:

  1. Using an already auto annotated version of NapoleonB on DNA Master gene 18 was confirmed to have the correct LORF.
  2. Synteny was also updated for genes 19 and 20.
  3. The rest of the genome was proofed as a class.

Results:

The synteny for genes 19 and 20 were updated using the phage KeaneyLin in addition to Nason. The rest of the genome was moderately corrected in order to fix entry errors.

Conclusions:

It can be confirmed that gene 18 was correct in its annotation. It can also now be concluded that genes 18, 19, and 20 do have synteny as shown in phamerator. It can also be concluded that the annotations for the phage NapoleonB are as of now correct.

Next Steps:

The next step will be to conduct an independent research project. We will also create a poster as a group in order to present at scholars week as a class, along with finalizing a class abstract.

February 20

2.20.19 Checking NapoleonB – Part 2

2.20.19 Checking NapoleonB – Part 2

Rationale: Since part of the annotation process is checking work, it is necessary to return to a complete annotation with fresh eyes and examine it again. Therefore, the class looked over the majority of the genes in NapoleonB that had been called once more to check to ensure annotations were properly done.

Tools/Procedure:

  • Genemark
  • DNA Master
  • NCBI BLAST
  • PhagesDB Blast
  1. Opened PhageNotes and DNA Master
  2. Checked and discussed each gene that was questionable
  3. Ran a separate Genemark with the correct species

Results:

The time in the lab today resulted in portions of calls being changed for a few genes that had been mistyped or had errors with the calls. The class had failed to use the proper species when using Genemark for the first time, so the correct species was used and some results were changed because of this.

Conclusions:

The main conclusion from today’s lab time was that the species is significant in the Genemark system. This was a previously forgotten fact, and it would have been detrimental to the annotations if it had gone unnoticed. Furthermore, today proved that one check was not enough, as the class found more discrepancies that were missed the first time around.

Next Steps:

During the next lab time, the independent projects will be examined more closely along with poster & abstract ideas for Scholar’s Week. Furthermore, it would be beneficial to examine NapoleonB with more detail than was done today.

February 20

February 20 2019 Checking NapoleonB Annotations and Poster Work

Purpose: The purpose of today’s lab is to re-check NapoleonB’s annotations and begin preparing for work on the Scholars Day poster.

Tools/Procedures:

Tools:

  • DNA Master
  • Phage Notes

Procedures:

  1. Annotations for NapoleonB were uploaded to DNA Master.
  2. Errors in start and stop positions were fixed and all genes were checked for correct length and position.
  3. Gene 1 and 2 were looked at, and it was determined that a reverse gene could not be added to replace gene 1. It is still uncertain if gene 1b will be added.
  4. Poster group work was started.

Results:
All of the genes for NapoleonB were checked again and looked at as a class. This helped to determine if the correct starts were chosen for each gene. It is still uncertain whether or not gene 1b will be added, since it is a reverse gene in between two forward genes.

Conclusions:
In conclusion, NapoleonB’s genome is still being checked. Checking the annotations multiple times will allow for more accurate results and for errors to be caught and corrected. Poster collaboration was begun and will be continued throughout the next few labs.

Future Work:
Future work will include finalizing NapoleonB annotations and completing a poster to present at Scholars Week.

February 20

Lab Day 9-10: Abstract and Full Gene Annotation Edits

Rationale

Create a rough draft for an abstract as a group and complete gene annotation and discuss any hard calls made.

Procedure

  1. Created abstract by combining other group members’ abstracts
  2. Fixed gene annotations as a class

Results/Next Steps
Certain genes were reannotated and different calls were made. Next time, we will make a final draft for the abstract and start designing a poster.

February 20

Sample abstract and Gene annotation correction for gene 44

02/18/19

Rationale: to acquire the fully annotated genome of Napoleon B

Procedure:

  1. DNA master was opened and Napoleon B was opened in DNA Master.
  2. Gene 44 was reevaluated
  3. NCBI was used to blast the gene and acquire genes in the database that matched with the query gene, which was used to find the possible similarity and function of the query gene
  4. Genemark was used to check the coding potential covered by the gene and the possible changes that could be made if possible to acquire the longest ORF possible.
  5. Phagesdb was used to blast the gene and acquire genes in the database that belonged to other phages that matched with the query gene, which was used to find the possible similarity and function of the query gene
  6. HHpred was used to predict the protein structure of the gene product, which was run through its database (Pfam and COG)for a possible matches with other proteins, which could be used to predict the function of the protein.
  7. Phamerator was used to compare the genome of napoleonb to other phages in the same category to compare syntony of the genes.
  8. phage notes was used for input of all the required information correcting the gene annotation.
  9. After, the abstracts of group members were compared and one sample abstract was submitted.

Results:

Gene 44 annotation:

SSC:30372 – 30815, CP:Yes, SCS:Both, ST:SA, BLAST-Start:Aligns with Circum gp46 NCBI BLAST q44:s1 1 6E-106, Aligns with Circum gp46 PhagesDB BLAST q44:s2 1 9E-84, Gap:8bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 3.102 -3.355 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Conclusion:

gene 44 has no known function.

Future steps

select abstract for scholars day submission

February 20

2/18 ~ Abstract Draft and Final Annotations of NapoleonB

Rationale: Finish up the final calls of NapoloenB and work on the abstract for the group poster

 

Materials:

  • DNA Mastering
  • PhagesDB
  • NCBI
  • Phamerator

 

Procedure:

  • Opened the Document with the genes that need extra annotations
  • Worked on the gene(s)
  • Worked in groups to create an abstract
  • Copy and pasted all the abstracts from everyone and created a new abstract
  • Submitted abstract as a group

Observations:

The abstract our group came up with

Worked on Gene 78, which has a large overlap with Gene 77

 

Conclusion/Next Steps: This work is leading to the completed annotation of NapoloenB. After this week (or next week), the entire genome of NapoleonB should be completely annotated. The next steps would be to agree on an abstract for the scientific poster and work on the content of the poster.

February 20

Revising Entire Annotation and Abstract Writing 2/20/19

Rationale: Now that we have completed our first draft of our annotation we’re going to take one last look before we hand it over to the TAs to revise it. We’re also going to write an abstract to submit for scholars day at Baylor.

Tools: Microsoft Word, DNAMaster, PhageNotes

Procedure:

  1. Scrolled through each gene that has been annotated after copying the PhageNotes documentation over to DNAMaster.
  2. Found a couple of mistyped starts and fixed them.
  3. Compiled each group members individual abstracts into one abstract using Word.

Results:

None.

Conclusion and Future Work: Now that we have finished our abstract we will put together a presentation of our findings of NapoleonB. Furthermore, we will begin individual projects soon.