findrRNA {microseq}

Finding rRNA genes

Description

Finding rRNA genes in genomic DNA using the barrnap software.

Usage

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

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.

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.

Value

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

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

readGFF, gff2fasta.

Examples

## 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)