January 25

1/23 ~ The Basics of Annotation via DNA Mastering

Rationale:

Learned how to evaluate reading frames, as well as how to calculate the gap or overlap between genes.

 

Materials:

  • Laptop
  • DNA Mastering Application
  • Learning Manual Powerpoint

 

Procedure:

  • Opened DNA Mastering on laptop
  • Entered in updated template code from PowerPoint (In preferences tab)
  • Auto-annotated Elesar and brought up the Open Reading Frames

Observations:

  • The spreadsheet shows indicates the endpoints of the 5′ and 3′, which can be used to calculate the gap or overlap between genes

Conclusion/Next Steps:

  • With this lab, learned more about DNA Mastering and how to operate the application. The next step(s) would be to auto-annotate Elesar
Category: Justin Yu | LEAVE A COMMENT
January 25

Elesar Auto Annotation 1/23/19 

Rationale:

The purpose was to learn about the features of DNA Master specifically about open reading frames using Elesar.  

Tools/Procedure:

  1. DNA Master was opened and the code, accessed through file then preference then local settings then new feature, was changed to “SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn”.  
  2. Elesar was added to DNA Master and Auto Annotated.  
  3. The ORF’s of Elesar were observed.  

Results: 

Auto Annotation of Elesar using a Fasta File was obtained using DNA Master. Reverse ORF’s represented by the highlighted portions were viewed.  

Conclusion: 

More features of DNA Master were learnt specifically about ORF’s. Concepts such as reading frames, gaps and overlaps were learnt as well.

Future Work:  

To acquire more knowledge about DNA Master’s features and understand the data presented for Elesar which will aid when annotating NapoleanB.

Category: Sona Subramanian | LEAVE A COMMENT
January 25

New template and autoannotation

Rationale:

to increase focus on certain genes and learn to annotate genes

Procedure:

  1. open  DNA master
  2. Preferences >Local settings >New Features
  3.  Type the following template command in the the “template to be installed box” :” SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn .
  4. check the “insert template into notes during Auto Annotation” box. Then Apply>OK
  5. Open FastA file for elesar using the following steps, File>open>FastA multiple sequence file> Choose Elesar.FastA
  6. click export on window with the extracted file and then choose Create sequence from this entry only.
  7.  to see the frames, go to DNA> Frames.
  8. then click ORF on the new window to see the highlighted genes.
  9. this is where time for lab ended.

Results:

auto annotation identified in 65 ORFs, of which 12 were reverse ORFS and 53 were forward ORFs, of which ORF 19 waas the longest.

Conclusion:

Reverse ORFs seem to be the most uncommon in the genome. more interpretation may be later required due to lack of porper knowledge as of now.

Future Steps:

the next lab will involve more work identifying genes and find gaps and overlaps between the auto annotated genes. It may involve identification of possible things that autoannotation missed.

 

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT
January 25

DNA Master Familiarization 1.23.19

Rationale:

To learn how to BLAST genomes and further gain understanding of DNA Master using the genome of the phage Elesar.

Procedure:

  1. Opened Elesar and adjusted local settings by inserting“SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn”.
  2. Autoannotated Elesar
  3. Opened ORFs for Elesar and viewed them

Results:

A greater understanding of DNA Master, specifically auto-annotation and ORFs,  was achieved through practicing with Elesar.

Conclusion:

My understanding of DNA Master was strengthened, which will be useful for further practice annotation on Elesar and the future annotation of NapoleonB’s genome.

Future Plans:

To continue to learn how to use DNA Master in order to annotate the genome of the phage Napoleon B and publish the annotations on PhageDB.

Category: Nathan Newton | LEAVE A COMMENT
January 24

Elsar Auto-Annotation 1/23

Rationale:

The purpose of today’s lab was to be introduced to the process of gene annotation. Elsar genome was annotated as an example for today’s lab to familiarize with the DNA Master program.

Procedure: 

DNA Master opened and preferences was opened > local settings > new feature. Checked “insert template into notes during annotation” and pasted: SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn. Elesar.fasta was opened and was auto-annotated.

Results:

Conclusions:

At first, all of the information was overwhelming, but once the TA’s cleared the confusion, work was done. The reading frames lines were easy to understand after an explanation of how DNA Master presents the reading frames.

Future plans: 

Learn more about DNA master and to begin annotation the genome of Napoleon B.

Category: Michael Lum, Uncategorized | LEAVE A COMMENT
January 24

1.23.19 Introduction to Annotation

1.23.19 Introduction to Annotation

Rationale: Today’s procedure was necessary to continue our understanding of DNA Master and gene annotation. Therefore, participating in the lecture, tweaking our DNA Master settings, and working through the QTM worksheet were prudent steps to being introduced to annotation.

Procedure:

  • Opened fasta file “Elesar” on DNA master
  • Adjusted template to be inserted during autoannotation
  • Auto-annotated Elesar genome
  • Used DNA–> Frames –> ORFs to identify all Open Reading Frames

Results:

Open reading frames of Elesar were found and briefly examined. Manual annotation of the genome has yet to be learned, so no further progress or understanding was achieved during this lab session.

Conclusion:

Since it was found to be possible to set up the DNA Master program for Open Reading Frame use, it will later be possible to find the Open Reading Frames on NapoleonB. This will be helpful as the genome is being processed and analyzed.

Future Plans:

Skills and lessons learned through the lecture, DNA Master steps, and QTM will later be helpful in analyzing NapoleonB, which will occur at a later date.

Category: Henry Burns | LEAVE A COMMENT
January 24

Elesar Annotations 1/23/2019

Rationale: auto-annotate elesar

Process:

  1. genome -> auto-annotate -> annotate
  2. auto-annotate with pecaan
    1. entered phage name “elesar”
    2. uploaded fasta file
    3. clicked “process”
  3. copied pecaan documentation, pasted it into documentation tab of dna master
    1. removed documentation previously there
    2. clicked “parse”, once directed to a new window, clicked the new “parse” button.

Results/Conclusion:

I could see a bar at the bottom with different colored “gene” arrows.

Future Steps: learn how to view more of the data after auto annotating

Category: Rachel Melone | LEAVE A COMMENT
January 24

DNA Day 2

23 January 2019 ✷ DNA Master Annotation

Rationale: DNA from Elesar was auto-annotated in order to differentiate the genes within the genome and lay the path for further research in the genome of a phage discovered in 2018.

Procedure

  • DNA Master was  opened and preferences was opened > local settings > new feature
    • checked “insert template into notes during annotation” and pasted “SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn” into box
  • Opened Elesar.fasta and auto-annotated it

Results

Conclusion

DNA master is a useful tool in which DNA can be analyzed and genes may be characterized. The processes and the program as a whole are still a bit confusing, but the overall idea of it is logical.

Future plans

This same method will be applied to Napoleon B, a phage isolated in 2018, in order to analyze its genome.

Category: Lily Goodman | LEAVE A COMMENT
January 24

Beginning An Annotation (1/23/19)

Rationale:

Insert template and learn more about basics of annotating.

Procedure:

  1. Opened DNA Master.
  2. Changed preference to insert template during auto-annotation.
  3. Auto-annotated Elesar.

Results:

The template was successfully inserted and auto-annotation was successfully performed with the template on Elesar as shown below.

Conclusion:

No difficultly was faced when auto-annotating Elesar. The conceptions learned today in lab were reading frames, how to calculate gaps and overlaps, and when a gap is required. A gap of at least 50 base pairs is required when the promoters are going in opposite directions.

Future plans:

Start analyzing the auto-annotation of Elesar and performing BLAST on Elesar.

Category: Kathryn Adkins | LEAVE A COMMENT
January 23

January 23, 2019 Beginning Annotations

Purpose: The purpose of today’s lab was to learn more about auto annotations and reading frames.

Tools/Procedures:

Tools:

  • DNA Master
  • Elesar FASTA file

Procedures:

  1. DNA master was opened
  2. The template was updated and saved for future work. The new template is SSC: CP: SCS: ST: Blast-start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn:.
  3. With the new preferences, Elesar was auto-annotated again.
  4. Elesar’s ORFs were examined.

Results:

  • Elesar was auto-annotated.
  • ORFs were examined.

Conclusions:

Elesar was auto-annotated successfully. The process of learning how to use the DNA Master program was continued.

Future Work:

For future work, the next steps will be to learn how to manually annotate and begin analyzing the auto-annotation of Elesar. Also, the process of learning DNA Master will be continued.

Category: Lucy Potts | LEAVE A COMMENT