Title: Annotation Practice on DNA Master

Date: 23 January 2019

Rationale: In this lab, the goal was to practice auto-annotation and experiment with some of the finer details regarding ORFs and gene overlap/gap. This lab also showed where the computer leaves ambiguity and how a gene must also be manually annotated.

Tools:

• Microsoft Surface Pro 5 Tablet
• DNA Master Software

Procedure: The FASTA file for phage Elesar was uploaded to the DNA Master software, exported, and “auto-annotated” in order to visualize individual ORFs and tRNAs. Once the Features list was visible, the Frames window was obtained by selecting the “Frames” option from the “DNA” drop down list. An annotation template was also inserted into the “Preferences.”

Results/Observations: The auto-annotated results showed the potential start and stop locations of potential genes (ORFs), a picture of the annotation is shown below (green values are forward reading frames, red values are reverse reading frames):

Out of 66 total found ORFs (and 1 tRNA), 11 were determined to be reverse reading frames while the other 55 were forward reading frames. Many ORFs were also observed to have gaps or overlap based on the start and stop location.

Conclusions/Next Steps: The gaps in ORFs are due to promoter regions in between each gene (instead of them being “backed up” against one another) while overlaps can be due to ambiguity in the computer’s annotation, which must be determined manually. The next steps for this lab are to start BLAST-ing the observed genes and comparing them (as proteins) against known sequences and functions. Also, the overlaps and gaps will have to later be accounted for manually.