BLAST Practice 1/28/2019

Rationale

The rationale behind these procedures is to learn how to annotate genes in DNA master by looking at BLAST results and using them to add information to the annotation notes.

Tools/Procedure

1. DNA Master was opened
2. A FASTA file was opened (File > Open> FastA Multiple Sequence File)
3. The contents of the file were exported (Export > Create Sequence from this Entry Only)
4. The contents of the file were Auto Annotated (Genome > Auto Annotate > click “yes”)
5. The reading frames were examined (Genome > Frames> click “ORFS” button)
6. Genes 1 and 2 were selected to BLAST (click on gene number > BLAST tab > Qblast against public database via NCBI server > Blast this gene)
7. Results from the BLAST were examined and used to start filling in the annotation notes

Results

The procedure detailed above was simply practice that yielded the above results. These results show what an auto-annotated genome would look like after being BLAST-ed before the annotation notes have been updated. These results allow one to asses whether or not a gene that was marked as a gene during auto-annotation is actually likely to be a gene and it gives a frame of reference for comparing the query DNA sequence to other DNA sequences.

Conclusion

The results of the practice BLAST can be seen above. These results allow one to compare the query DNA sequence to similar sequences of DNA as one means of verifying that a gene is a real gene, and as a way to help understand the function of the gene and potentially identify areas of conserved DNA in multiple genomes.

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 likely BLAST all of the genes in Napoleon B and compare those results to genemark and the auto-annotation results in order to asses that all genes are in fact genes and to fully annotate the genome.