Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.
% barrnap --quiet examples/small.fna ##gff-version 3 P.marinus barrnap:0.6 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA P.marinus barrnap:0.6 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA P.marinus barrnap:0.6 rRNA 358433 358536 7.5e-07 + . Name=5S_rRNA;product=5S ribosomal RNA