BAsic Rapid Ribosomal RNA Predictor
Torsten Seemann - firstname.lastname@example.org - @torstenseemann
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.
* Tarballs: https://github.com/tseemann/barrnap/releases/
* Source: https://github.com/tseemann/barrnap
% cd $HOME
% tar zxvf barrnap-0.X.tar.gz
% echo "PATH=$PATH:$HOME/barrnap-0.x/bin" >> .bashrc
(logout and log back in)
% barrnap --quiet examples/small.fna
P.marinus barrnap:0.7 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA
P.marinus barrnap:0.7 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA
P.marinus barrnap:0.7 rRNA 358433 358536 7.5e-07 + . Name=5S_rRNA;product=5S ribosomal RNA
% barrnap -q -k mito examples/mitochondria.fna
AF346967.1 barrnap:0.7 rRNA 643 1610 . + . Name=12S_rRNA;product=12S ribosomal RNA
AF346967.1 barrnap:0.7 rRNA 1672 3228 . + . Name=16S_rRNA;product=16S ribosomal RNA
Barrnap does not do anything fancy. It has HMM models for each different rRNA gene.
They are built from full length seed alignments.
* Perl >= 5.6
* HMMER >= 3.1b
Barrnap is free software, released under the GPL (version 3).
## Comparison with RNAmmer
Barrnap is designed to be a substitute for RNAmmer. It was motivated by
my desire to remove <A HREF="https://github.com/tseemann/prokka">Prokka's</A> dependency on RNAmmer
which is encumbered by a free-for-academic sign-up license, and by RNAmmer's
dependence on legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now.
RNAmmer is more sophisticated than Barrnap, and more accurate because it uses HMMER 2.x in glocal alignment mode whereas NHMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical rRNA genes in a few seconds (in bacteria), but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from Rfam, Silva and RefSeq.
## Data sources for HMM models
12S RefSeq (MT-RNR1, s-rRNA, rns)
16S RefSeq (MT-RNR2, l-rRNA, rnl)
TODO: [Sajeet Haridas]
LSU 35S ?
21S (multiple exons)
LSU ~2500bp 28S ?
SSU ~1500bp 16S ?
Plastid [Shaun Jackman]
## Where does the name come from?
The name Barrnap was originally derived from _Bacterial/Archaeal Ribosomal RNA Predictor_.
However it has since been extended to support mitochondrial and eukaryotic rRNAs, and has been
given the new backronym _BAsic Rapid Ribosomal RNA Predictor_.
The project was originally spawned at CodeFest 2013 in Berlin, Germany
by Torsten Seemann and Tim Booth.