Finding rRNA genes
Finding rRNA genes in genomic DNA using the barrnap software.
findrRNA(genome, bacteria = TRUE, cpu = 1)
genome |
A table with columns Header and Sequence, containing the genome sequence(s).. |
bacteria |
Logical, the genome is either a bacteria (default) or an archea. |
cpu |
Number of CPUs to use, default is 1. |
The external software barrnap is used to scan through a prokaryotic genome to detect the rRNA genes (5S, 16S, 23S). This free software can be installed from https://github.com/tseemann/barrnap.
A GFF-table (see readGFF for details) with one row for each detected
rRNA sequence.
The barrnap software must be installed on the system for this function to work, i.e. the command system("barrnap --help") must be recognized as a valid command if you run it in the Console window.
Lars Snipen and Kristian Hovde Liland.
## Not run:
# This example requires the external barrnap software
# Using a genome file in this package.
genome.file <- file.path(path.package("microseq"),"extdata","small.fna")
# Searching for rRNA sequences, and inspecting
genome <- readFasta(genome.file)
gff.tbl <- findrRNA(genome)
print(gff.table)
# Retrieving the sequences
rRNA <- gff2fasta(gff.tbl, genome)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.