Annotation Practice and Function Calling 2/4/2019

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 including looking at amino acid sequences in an attempt to determine protein function.

Tools/Procedure

1. DNA Master was opened and the previous Elsar file was loaded
2. Annotation notes for genes 10 and 11 were corrected for the following fields – SSC: CP: SCS: BLAST-Start: Gap: LO: RBS:
3. NCBI, Phages DB, and HHPred systems were used to BLAST amino acid sequence for genes 10 and 11
4. The results of these BLASTs were recorded in the results seen below for the following annotations – SIF-BLAST: SIF-HHPred:

Results

Gene 10 – SSC:7514,7813 CP: No SCS: both ST: BLAST-Start: no significant BLAST alignments Gap: 15 bp LO: yes RBS: Kibler7, Karlin Medium, 2.299, -4.080, yes F: SIF-BLAST: NKF, no matches with e values below 10-7 SIF-HHPred: NKF, no matches with a probability above 90% SIF-Syn: NFK

Gene 11 – SSC: 7829, 8230 CP: No SCS: Both ST: BLAST-Start: Aligns with Arthrobacter phage Ryan, NA, NCBI, q1:s1, 95%, 2e-70 Gap: 15 LO: yes RBS: Kibler7, Karlin Medium, 2.565, -3.515, no F: SIF-BLAST: head-to-tail adapter, NCBI, Arthrobacter phage Ryan, AYN59006.1, 95%, 2e-70 SIF-HHPred: NKF, Pfam, Phage_Gp19, PF09355.10, 92.8%, 99.75 SIF-Syn: NFK

Conclusion

These results show the completed structural annotation notes for genes 10 and 11. Of these genes, only gene 11 has significant protein BLAST results, meaning that gene 11 has a sequence of DNA very similar to other DNA found in bacteriophage. These similarities suggest that gene 11 codes for a head-to-tail adapter. However, gene 10 did not have significant BLAST results and therefore are not highly conserved among known genomes. For the time being this means that there is no known function for gene 10 and it will remain a hypothetical protein.

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. I will also BLAST the amino acid sequences to look for similarities to proteins with known functions. I will also be sure to fill in all of the basic information that is required in the annotation notes to make scientific inquiry easier in the future.