4 February 2019 ✷ DNA Annotation

Procedure

• The FASTa file for Elesar was opened and auto-annotated.
• The “features” tab was opened and within the “notes” box, the code for genes 2 and 3 were annotated
  • errors from the prior lab were corrected; for gene 2, the “blast” command was corrected (the phage name and protein number were combined to fix the error). For gene 3, the “blast” command was corrected by swapping the order of the % match and the ratio, RBS was redone, and CP was adjusted from “yes” to “no” because it was incorrect originally.
• The SIF-BLAST and SIF-HHPred commands were annotated:
  • The product codes were run through phagesdb blast and HHPred (+ COG and PFam databases) and that information was added to the annotation as indicated by NCBI.
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• PhagesDB results:
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Results

the updated annotations for each gene are as follows:

Gene 2

SSC:[346,690] CP:[yes] SCS:[both] ST: BLAST-Start:[Andrew_1, phagesdb, 1:1, 62%, 3e-17] Gap:[8bp overlap] LO:[no] RBS:[Kibler7, Karlin Meduim, 3.167, -2.177, no] F:[] SIF-BLAST:[terminase large sububit, phagesdb, Andrew_1, MH834595, 62%, 3e-17] SIF-HHPred:[Phage Terminase, PFam, n/a, PF03354.15, 95%, 98.68] SIF-Syn:[]

Gene 3

SSC:[954,1352] CP:[no] SCS:[Glimmer] ST: BLAST-Start:[Ryan_4, phagesdb, 1:1, 100%, 6e-70] Gap:[263bp gap] LO:[yes] RBS:[Kibler7, Karlin Medium, 2.853, -3.115, no] F:[] SIF-BLAST:[DNA binding protein, phagesdb, Ryan_4, MH834627, 100%, 6e-70] SIF-HHPred:[Transposase, COG, n/a, COG4584, 95%, 98.75] SIF-Syn:[]

Conclusion

Annotation is useful in research in comparing different genes within differing species that potentially contain the same gene. Determining the function of genes based on other’s research and recorded data is useful in speeding up the process of studying a genome.

Future plans

This same method will be applied to Napoleon B, a phage isolated in 2018, in order to analyze its genome.