knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(tzara) library(inferrnal) library(LSUx) library(ShortRead)
The sample sequences are the 37S pre-rDNA (including SSU, ITS1, 5.8S, ITS2, LSU) from eleven Saccharomyces genomes.
rDNA37 <- readFasta(system.file(file.path("extdata", "RDN37.fasta"), package = "tzara"))
Find the 32S region
pos <- lsux(rDNA37)
Choose the region from 5.8S to LSU5 (prior to the beginning of D5).
extract_region(rDNA37, positions = pos, "5_8S", "LSU5")
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