microseq (version 1.3)

findrRNA: Finding rRNA genes

Description

Finding rRNA genes in genomic DNA using the barrnap software.

Usage

findrRNA(genome.file, bacteria = TRUE, cpu = 1)

Arguments

genome.file

A fasta-formatted file with 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.

Value

A gff.table (see readGFF for details) with one row for each detected rRNA sequence.

Details

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.

See Also

readGFF, gff2fasta.

Examples

# NOT RUN {
# This example requires the external barrnap software
# Using a genome file in this package.
xpth <- file.path(path.package("microseq"),"extdata")
genome.file <- file.path(xpth,"small_genome.fasta")

# Searching for rRNA sequences, and inspecting
gff.tbl <- findrRNA(genome.file)
print(gff.table)

# Retrieving the sequences
genome <- readFasta(genome.file)
rRNA <- gff2fasta(gff.tbl, genome)
# }
# NOT RUN {
# }