February 22

Annotation Check for NapoleonB & Abstract Draft 2.18.19

Rationale:

To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. PhageNotes is also introduced as a convenient way to annotate genes and revising them. Abstract for the presentation was discussed, since an abstract should concisely inform readers or poster viewers the important points of the research.

Materials:
  • Laptop
  • DNA Mastering Program
  • Gene sequence of phage NapoleonB
Procedure:
  1. Some of the red flags on gene annotations were reviewed, gene 78 was examined since it has a 35 bp overlap with the previous gene.
  2. Abstract draft was discussed and written in a small group and submitted at the end of the lab.
Results/Next Steps:

Abstract Draft:

Arthrobacter is a bacteria genus commonly found in soil and sewage that can be utilized in bioremediation and degradation of pesticides. The HHMI SEA-PHAGE initiative at Baylor University (BEARS in the SEA) used Arthrobacter sp. ATCC 21022 as a host to isolate Arthrobacter phage found around the Baylor campus. From over 60 soil samples collected, 8 were positive for Arthrobacter phage, six were submitted to PhagesDB, and novel Arthrobacter phage NapoleonB was sequenced. The genome of the bacteriophage was annotated using bioinformatic tools. Of the 100 predicted genes of Bacteriophage NapoleonB, 72 of the genes had no clear functionality. The predicted genes have been put into a database and used to cross-reference with other phages. Further research could be conducted in order to determine the functions of the unknown proteins.

The gene 78 call wasn’t changed in order to cover the coding potential in the overlapped region.

In the next lab, final gene annotations and abstract draft would still be the main objective.

Category: Yang-En Yu | LEAVE A COMMENT
February 22

2/20/19 NapoleonB Final Checks

Rationale:

The purpose of today’s lab was to move through the genome as a class to catch any last mistakes before Leo and Lathan comb through the genome before submitting.

Tools:

  • DNA Master
  • NCBI BLASTp

Procedure:

  • As a class, the lab reviewed any gene that raised any red flags while scrolling through the annotation.
  • Gene 61 raised a red flag regarding the selected start as there was one longer open reading frame that could have been selected.
  • Re-checked and fixed the initial gene annotation on 61.

Results:

  • Original Glimmer call @bp 36690 has strength 7.46; GeneMark calls start at 36693
    SSC:36690 – 37253, CP:Yes, SCS:BothGL, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Mudcat gp57 NCBI BLAST q2:s1 0.99 3E-17, Aligns with Mudcat gp57 PhagesDB BLAST q2:s1 0.99 1E-108, Gap:14bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 3.118 -2.454 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF
  • Blast Results

Conclusions:

It was decided to pull the gene back to the start at 36690 base pairs. This correction was decided as pulling the gene back resulted in a better query coverage with the BLASTp hit as a q1:s1 instead of a q1:s16 that the other start yielded.

Next Steps:

The next steps for this experiment are to finalize the gene calls for NapoleonB and submit a final abstract for Scholar’s Week.

Category: Uncategorized | LEAVE A COMMENT
February 22

2/18/19 NapoleonB Annotation Checks

Rationale:

The purpose of today’s lab was to go over genes that were marked as red flags and to justify the annotations or fix them.

Tools:

  • DNA Master
  • NCBI BLASTp
  • PhagesDB BLAST

Procedure:

  • Gene 64 raised questions regarding the open reading frame selected for the start.
  • Once I was assigned the gene, I looked into it to try and justify the selected call.

Results:

  • Original Glimmer call @bp 35903 has strength 11.27
    SSC:35903 – 36703, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage KeaneyLin gp58 NCBI BLAST q1:s1 0.99 0, Aligns with Arthrobacter Phage KeaneyLin gp58 PhagesDB BLAST q1:s1 1 e-155, Gap:4bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.007 -3.956 No, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Conclusions:

It was decided to keep the gene were it was originally called as pulling the gene further back would have violated the guiding principle of phage annotation by creating too large of an overlap in the phage genome. Although it is not the longest open reading frame, it is as far back as possible without violating the guiding principle.

Next Steps:

The next steps are to continue checking final gene annotations of NapoleonB and review abstract submissions for Scholar’s Week.

 

Category: Uncategorized | LEAVE A COMMENT
February 22

Poster Designs and NapoleonB Annotation Changes (2/20/19)

Rationale:

The purpose of the lab was to review the annotations and good poster design ideas.

Tools: 

  • DNA Master 
  • GeneMark  
  • NCBI Blast 
  • PhagesDB Blast 
  • Phamarater 
  • HHPred 
  • Phage Notes 

Procedure: 

  1. Gene Annotations for NapoleonB were reviewed.  
  2. Gaps in the Open Reading Frames were discussed and reviewed.  
  3. Changes were made to Gene 96 of Napoleon B.  
  4. New annotation was updated to PhageNotes.  
  5. Important aspects of a scientific report were reviewed.  

Results: 

Annotation of Gene 96:  

Conclusion: 

Gene 96 was annotated again since a better value and hit was found. The start value of gene 14 was inputted incorrectly, so edits were made.  

Future Work:  

Groups will be assigned for the poster project and designs for the poster will be started.  

Category: Sona Subramanian | LEAVE A COMMENT
February 22

Evaluating NapoleonB’s Gene 96 and Group’s Final Abstract (2/18/19)

Rationale:

The purpose of the lab was to revise NapoleonB’s genes, and to create a final abstract.  

Tools:  

  • DNA Master 
  • GeneMark  
  • NCBI Blast 
  • PhagesDB Blast 
  • Phamerater 

Procedure: 

  1. Groups were assigned for annotations and abstract.  
  2. NapoleonB’s Gene 96 Annotation was re-evaluated because of a large gap between gene 95 and 96.  
  3. Coding potential between gene 95 and 96 was viewed and evaluated.  
  4. A place which appeared to have a high coding potential on GeneMark was added to DNA Master as a test gene.  
  5. Results were collected with the product of the test gene on PhagesDB and NCBI Blast.  
  6. Phamerater was used to compare different AM cluster phages.  

Results: 

The results on PhagesDB and NCBI Blast displayed that there were no hits for the particular coding region, which was a reverse ORF. Therefore, the annotation of Gene 96 was not changed.  

Conclusion:

More knowledge was acquired on DNA Master about how to test gaps and see if there was a hit. Even though GeneMark displayed a high coding potential on the graph, the results displayed no hits.  

Future Work:

Next class we will re-evaluate the genes and recheck the annotations of the genes.  

Category: Sona Subramanian | LEAVE A COMMENT
February 22

Checking NapoleonB’s Genes 2/20/19

Title: Checking NapoleonB’s Genes

Date: 20 February 2019

Rationale: Before the final annotations of NapoleonB are sent in, the genes must be checked for accuracy and any abnormalities double checked and justified.

Tools Used:

  • DNA Master
  • NCBI BLASTp
  • PhagesDB BLAST
  • GeneMark

Procedure:

  • Genes 47 and 48 were checked to ensure that the chosen start was justified by BLASTing and comparing gene products. Other abnormal calls were also checked by the class and any mistakes fixed as observed.

Results/Observations: The results from NCBI and PhagesDB showed that the starts chosen (not the longest available ORF) were justified (due to q1:s1) as well as a worse blast hit when the reading frame was pulled back. No changes were made to the original calls.

Conclusions/Next Steps: Once a final abstract is selected, poster design will commence as well as possibly another check of the NapoleonB annotations to ensure accuracy. Individual research projects will also start soon.

 

Category: Cooper Johnson | LEAVE A COMMENT
February 22

Abstract Composition and Editing 2/18/19

Title: Abstract Composition and Editing

Date: 18 February 2019

Rationale: The purpose of this lab session was to review and finalize a draft of an abstract to submit for Scholars Day

Procedure: The contents of 4 different abstracts were compiled into one final abstract and submitted for review

Results: A final abstract regarding the discovery, purification, and isolation of NapoleonB along with the characterization of its genes was compiled and finalized. The brainstorming process for a Scholars Day poster was also started.

Conclusions/Next Steps: The other abstracts will be considered and compiled in order to ensure that the best possible abstract is submitted to represent the cohort at Scholars Day.

Category: Cooper Johnson | LEAVE A COMMENT
February 22

Checking NapoleonB (2/20/19)

Rationale: Checked NapoleonB’s annotations as a class for mistakes. Started brainstorming ideas for the poster.

Tools:

  • DNA Master
  • GeneMark
  • phage notes

Procedure:

  1. Checked for mistakes by scrolling through the frames window in DNA Master.
  2. Used GeneMark graph to check that all coding potential was covered.
  3. Checked annotations in phage notes.
  4. Started brainstorming what belongs on the poster and what format to use.

Results:

NapoleonB’s genes 25-28 covered all coding potential. No corrections were made.

Conclusion:

After brainstorming with the group, it was decided that the methods section should be presented in a flow chart for easy comprehension. Use of columns also would allow for better organization. The color scheme being used should be easy on the eyes. The TEM, gel, and phamerator should be presented on the poster. The poster should also include the final version of the abstract; the names of the researchers,  TAs, and LAs; and a title.

Future Work:

Finish abstract and start designing the poster.

Category: Kathryn Adkins | LEAVE A COMMENT
February 22

2/20 ~ Final Annotations and Abstracts

Rationale: Finish (As a class) looking at the annotations of NapoleonB, making sure any gaps are accounted for, as well as work on the abstract

 

Materials:

  • DNA Mastering
  • PhagesDB
  • NCBI
  • GeneMark
  • Phamerator

 

Procedure:

  • Opened DNA Mastering
  • Opened NapoleonB file and opened frames
  • Opened NapoleonB Phagenotes and followed along with the class, accounting for each gap in genes
  • Assisted in fixing any genes that needed to be pulled back or up
  • Looked at all submitted abstracts and determined an abstract that worked best

Observations:

The coding potential of gene 96, which was one of the genes deliberated about during lab

The frames view of gene 96, which has a large gap upstream

 

Conclusion/Next Steps: The annotations of NapoleonB are almost done. After the last few changes, NapoleonB will be checked once more by the TA’s and then confirmed. The abstract of the poster will continue to be worked on.

Category: Justin Yu | LEAVE A COMMENT
February 21

Poster design and final checking of annotation

02/20/19

Rationale:

to acquire the fully annotated genome of Napoleon B

Procedure:

  1. reviewed the annotated genome with the class and we were instructed to make possible changes
  2. Talked about poster design and the important elements of  making a scientific poster.

Results:

3 corrections were made to the genes of Napoleon B and all genes were reviewed.

Conclusion

the genome is now fully annotated and ready for review.  there are many gaps in the genome , which is very peculiar. something can be looked into

Future steps:

work on individual research projects

 

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT