January 18

DNA Master Software Install and Tutorial 1.16.19

Rationale:

To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. Phage Elesar was picked to be the sequence for the tutorial, in order to familiarize with the functions and features of the software.

Materials:
  • Laptop
  • DNA Mastering Program
  • Gene sequence of phage Elesar
Procedure:
  1. Found the link that directs to the website containing the link for DNA Master download.
  2. Downloaded the file and attempted to install to laptop.
  3. Could not install and run the software on the laptop, the tutorial was done until before gene blasting using phage sequence Elesar.
Observations:

The error message indicated that it was a decompression failure, while other file download extractions testing were successful DNA Master couldn’t be installed. Memory space on the hard drive and TEMP file was checked and cleared for the files after extraction, however, the problem remained.

Results/Next Steps:

The features in DNA Master was introduced in this lab, however, the software installment on the laptop was ultimately unsuccessful. A solution has yet to be found, the goal is to fix the error and have a operational DNA Master on the laptop by the next lab.

Category: Yang-En Yu | LEAVE A COMMENT
January 18

Beginning DNA Master 1.16.18

Rationale:

The purpose of this lab was to familiarize myself with DNA Master with the goal of annotating the genome of the phage NapoleonB.

Procedure/Tools:

  • DNA Master
  1. The FastA file for the phage Elesar was downloaded.
  2. DNA Master was opened and the FastA file for Elesar was selected and opened.
  3. An auto-annotation was run for Elesar’s genome.

Results:

The genome of Elesar was auto-annotated revealing 66 genes with 11 reverse genes and 55 forward genes. DNA Master had been previously downloaded and setup.

Conclusion/Future Work:

From the data collected it can be concluded that Elesar has 66 genes, 55 of which are forward and 11 of which are reverse, a greater understanding of DNA Master was also achieved. In the future, I will continue to annotate Elesar in order to become more familiar with DNA Master and the annotation process in order to successfully annotate NapoleonB.

Category: Nathan Newton | LEAVE A COMMENT
January 18

1.16.18 Starting DNA Master

1.16.18 Starting DNA Master

Rationale: In Wednesday’s lab session (after the presentations), it was found to be important to set up DNA master and practice the procedure for auto-annotating bacteriophage genomes.

Tools/Procedure: In Wednesday’s lab, only DNA master and its auto-annotation feature was used.

Results: The genome for Elesar was successfully auto-annotated. The program had already been downloaded before the lab had begun and the steps for preparing the program had already been completed. The genome was downloaded from phagesdb.org, then it was auto-annotated. This was all that time permitted during the time in the lab.

Conclusion: The result of the lab is that I successfully learned how to auto-annotate a genome after downloading on phagesdb.org. There were no difficult decisions to be made, as the genome was not processed fully or annotated further than the auto-annotation.

Future Work: In the following labs, I plan to use the auto-annotation technique on NapoleonB to process that genome. I also plan to build on that basis by learning more about manually editing the auto-annotation. This will ideally permit a good understanding of the phage’s genome and genes after using DNA master on the genome.

Category: Henry Burns | LEAVE A COMMENT
January 18

Exploring DNA Master 1/16/19

Title: Exploring DNA Master

Date: 16 January 2019

Rationale: The purpose of this lab was to explore DNA Master and begin the process of learning how to annotate phage genomes. With the skills needed to navigate and use DNA Master, many different conclusions can be drawn from the output including protein function, nucleotide sequence, and more.

Tools:

  • Microsoft Surface Pro Tablet
  • DNA Master Software

Procedure: A presentation on a specific bacterial infection treatment by means of phage therapy was done before installing and running DNA Master for the first time. Due to technical difficulties, DNA Master did not run perfectly the first time. The program was uninstalled and reinstalled, as well as restarted multiple times to ensure that all necessary updates were completed and the necessary procedures could be run. Finally, after a reinstalling of the program,DNA Master began to run reliably. Once the program was running, the FastA file for bacteriophage Elesar was downloaded and run by the program. Once the FastA displayed the nucleotide sequence for the phage, an auto-annotation was selected and run. A BLAST was unable to be completed at the time of writing.

Observations/Conclusions:

  • Elesar yielded 42,954 nucleotides and 67 possible genes
  • 66 of the recognized possible genes were classified as ORF’s (open reading frames) while the one remaining feature was classified as “RNA”
  • The program lists all of the recognized features and color codes them as to distinguish whether or not it is a forward or reverse reading frame
  • Below is a screenshot of the listed genes that DNA Master recognized

 

  • A conclusion that can be made about this lab is that DNA Master has many different features and potential methods to map out and recognize characteristics of a genome, once the necessary skills are learned to navigate the program.

Next Steps: 

  • The next step after learning how to use DNA Master is to analyze bacteriophage NapoleonB in order to discover its sequence and protein function.
  • Continue to monitor and troubleshoot the DNA Master program for any future problems.

 

Category: Cooper Johnson | LEAVE A COMMENT
January 17

Lab Day 1: Begin DNA Master

Rationale

The purpose of this lab was to get familiar with the DNA Master program and start annotating the genome sequence of Elesar.

Tools

  • personal laptop
  • DNA Master
  • Elesar fastA file

Procedure

  1. DNA Master wasd downloaded unto personal computer and updated
  2. Elesar file was downloaded and auto annotated through DNA Master
  3. Made sure everything on that file had the coordinates and was annotated properly.

Observations/Results

This process took awhile to get the sequence auto annotated correctly. The green colored is forwards ORFs and the red colored are the reverse ORFs. The second pic showed each line as possible start codons.

Next Steps

Learn more and get used to using DNA Master. Soon NapleonB will be auto annotated and learn more about its genome.

Category: Soo-Un Jeong | LEAVE A COMMENT
January 17

DNA Master Installation and Auto Annotation 1/16/19

Rationale

Today we presented our phage therapy powerpoints, downloaded DNA Master onto our personal computers, and began practicing annotating DNA on the genome of phage Elesar.

Procedure

  • Various groups from the classes presented their articles on phage therapy.
  • DNA Master was downloaded onto the computers.
  • A FastA file was downloaded for Elesar from PhagesDB.
  • Elesar was uploaded to DNA Master and was auto-annotated.

Observations/Results

DNA Master revealed that there are 66 ORFs in Elesar. There are 11 reverse ORF of the 66 documented. There are also 55 forward ORFs. Some tasks on DNA Master took a large amount of time to process, however, each task ran smoothly.

Conclusion/Next Steps

I really look forward to learning more about DNA Master and the different discoveries that can be made while using the program. In the coming months, we will dive more into the program and learn more about phage NapoleonB. We also will attempt to improve our presentation skills throughout the semester.

Category: Emily Gaw | LEAVE A COMMENT
January 17

1/16/19 ~ DNA Master and Bioinformatics

Rationale:

The purpose of today’s lab was to learn how to operate DNA Master as well as present the presentation we made on Monday about the articles pertaining to phage therapy.

 

Materials:

  • Laptop / Desktop Computer
  • DNA Mastering Program

 

Procedure:

Began class with presentations regarding the articles on phage therapy. Then installed the DNA Mastering application on laptop. Updated the application and then downloaded the Elesar FASTA file from the PhagesDB website. Elesar was then auto-annotated by DNA Mastering.

 

Observations:

The frames in green represent a forward ORF, while the red represents a reverse ORF

Although there were a few problems initially, the FASTA file Elesar was successfully annotated

 

Results/Next Steps:

DNA Mastering auto-annotated Elesar and resulted in ORF’s. Although most of it is confusing and gibberish on the screen, with enough time and exposure/practice, the class’ genome will be able to be annotated. Hopefully, the lab can began to annotate NapoleonB and start determining functions of the genes.

Category: Justin Yu | LEAVE A COMMENT
January 17

DNA Day 1

16 January 2019 ✷ DNA Master

Rationale: DNA Master was downloaded onto personal computers in order to practice annotating DNA.

Procedure

  • Elesar, a previously discovered phage within PhagesDB, had a recorded DNA sequence file that was downloaded and then annotated through DNA master.
  • The preferences on DNA Master were updated to use different colors and base pairs that were to be included were updated; the program was also given permission to use the HHMI database.
  • The FastA file for Elesar was opened and run through the program, producing the images seen below.

Observation, Results, Data

The genome of Elesar is larger than I had imagined, given the small size of a bacteriophage. The sheer length of its genetic code is impressive to see written out as it is in DNA master.

Interpretations, Conclusion, Next Steps

In the following lab periods, the genome of phages discovered within the 2018-19 cohort of Baylor Univerity’s SEAPHAGES group will be analyzed and annotated.

Category: Lily Goodman | LEAVE A COMMENT
January 17

Auto Annotation and DNA master installation

1/16/19

Rationale:

To install and use DNA master to  auto annotate and analyse the genome of phage elesar.

Tools Used:

  • Personal Laptop
  • DNA master

Procedure:

  1. DNA master was downloaded and installed onto personal laptop.
  2. The following steps were followed to go to local settings, File > Preferences> Local settings> Directories
  3. Archive file settings were changed to a location where it would be easier to find
  4. The color settings for tRNA, tmRNA and ORF are changed and all the changes are applied
  5.  the elesar genome file was opened in DNA master using the following, File>Open>FastA multiple sequence file
  6. the following steps were followed, Export> Create sequence from this entry only>Genome>Auto Annotate
  7. this is where the day ended.

Observations:

The operation of DNA master is difficult and will take a great deal of practice. Elesar has 66 genes, of which one was tRNA and the rest are ORF genes.

Results:

successful auto annotation was performed on the genome sequence. ORFs on the gene sequence were marked as shown above.

Conclusions and Future Steps:

Currently, no conclusions can be drawn from this data due to the lack of the knowledge to do so. more practice and augmentation is required to better work with this software.

 

 

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT
January 17

Annotation and Introduction to DNA Master (1/16/19)

Rationale:

Presented scientific article to the class and set up DNA Master on laptop to use for future genome analysis.

Procedure:

  1. Installed and updated DNAMaster on laptop.
  2. Downloaded FASTA files for Elesar off phagesdb.org.
  3. Performed and analyzed auto-annotation of Elesar.

Observations:

Elesar has 66 genes of which 11 have reverse ORFs and 55 had forward ORFs.

Compared to all of Elesar’s other genes, gene 19 had the longest length which was 4824 nucleotides.

Results:

DNA Master was successful downloaded onto laptop. Also, was able to successfully access ORF Analysis of Elesar as shown below.

Conclusion and Next Steps:

Although my laptop screen looks like gibberish to me now, I look forward to learning and using DNA Master to annotate and perform analyses on NapoleanB. Also, I look forward to improving my presentation skills. I hope to become more familiar with DNA Master by annotating and BLAST Elesar.

Category: Kathryn Adkins | LEAVE A COMMENT