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.
This exercise is part of the course
Introduction to Bioconductor in R
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Print rnaframesZikaSet
___
# Translate rnaframesZikaSet
AAzika6F <- ___(___)
AAzika6F