DNA Master Annotation Practice 1/23/2019

Rationale

The rationale behind these procedures is to learn how to annotate genes in DNA master while also adding several features to the auto-annotation sequence.

Tools/Procedure

1. Open DNA Master
2. Open File> Preferences > Local Settings > New Feature > add the following code:
   SSC: CP: SCS: ST: BLAST-Start: Gap: LO: RBS: F: SIF-BLAST:
   SIF-HHPred: SIF-Syn
3. Open a FASTA file (File > Open> FastA Multiple Sequence File)
4. Export contents of the file (Export . Create Sequence from this Entry Only)
5. Auto Annotate contents of the file (Genome > Auto Annotate > click “yes”)
6. Examine reading frames (Genome > Frames> click “ORFS” button)
7. Compare gene locations paying attention to gaps and overlap

Results

The procedure detailed above was simply practice that yielded the above results. These results show what an auto-annotated genome would look like for future reference in later annotations. They also show the 6 possible reading frames on which genes can be found. The genes shown highlighted in green signify genes read in the forward direction while genes highlighted in red show reverse genes. These results allow me to compare gaps and overlaps between genes to determine in the auto-annotation was accurate in determining genes in the genome.

Conclusion

The results of the practice auto-annotation can be seen above. An annotated genome that can be reviewed by a human. By examining the reading frames one can determine if the genes marked in the auto-annotation are likely to be legitimate coding strands for genes or not. While there were no tough calls to make in today’s lab, genes 25 and 22 look unlikely to be legitimate and this will need to be further examined.

Future plans

In the future, I will use what I learned how to do in this procedure when I am analyzing the genome from Napoleon B. I will perform auto-annotations as well as many other forms of testing on that genome in the lab periods to come. I will also likey study genes 25 and 22 to ensure that my initial reaction to their legitimacy is accurate.