Exercise

Finding a conserved region within six frames

Congratulations on getting this far!

Now you will be able to look for the NS5 protein sequence in the Zika virus sequence. The NS5 is a very conserved virus protein. It was downloaded and loaded for you from Uniprot.

The Zika virus DNA sequence has been transcribed into an RNAStringSet, called rnaframesZikaSet. The set has six reading frames (one per sequence) for you to translate into amino acids. When doing the search, you will set the max.mismatch argument in your call of vcountPattern() to add flexibility to your search.

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Print rnaframesZikaSet.
Translate all of the 6 reading frames into amino acids.