Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan 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. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.
See which versions of barrnap are available:
$ module avail barrnap
Load one version into your environment and run it:
$ module load barrnap/0.9 $ barrnap
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz $ tar xf 0.9.tar.gz $ cd barrnap-0.9 $ sudo mkdir -p /export/apps/barrnap/0.9 $ sudo cp -r bin db examples LICENSE* /export/apps/barrnap/0.9/