microseq (version 2.1.6)

findrRNA: Finding rRNA genes

Description

Finding rRNA genes in genomic DNA using the barrnap software.

Usage

findrRNA(genome, barrnap.exe = "barrnap", bacteria = TRUE, cpu = 1)

Value

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

Arguments

genome

A table with columns Header and Sequence, containing the genome sequence(s).

barrnap.exe

Command to run the external software barrnap on the system (text).

bacteria

Logical, the genome is either a bacteria (default) or an archea.

cpu

Number of CPUs to use, default is 1.

Author

Lars Snipen and Kristian Hovde Liland.

Details

The external software barrnap is used to scan through a prokaryotic genome to detect the rRNA genes (5S, 16S, 23S). The text in barrnap.exe must contain the exact command to invoke barrnap on the system.

See Also

readGFF, gff2fasta.

Examples

if (FALSE) {
# 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)
}