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BAsic Rapid Ribosomal RNA Predictor

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 newnhmmer 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.

• Perl 5.xx (core modules only)
• nhmmer (part of HMMER 3.x)
• bedtools >= 2.27.0

InstallConda orMiniconda:

conda install -c bioconda -c conda-forge barrnap

InstallHomebrew (macOS) orLinuxbrew (Linux).

brew install brewsci/bio/barrnap

This will install the latest version direct from Github.You'll need to add thebin directory to yourPATH.

cd $HOMEgit clone https://github.com/tseemann/barrnap.gitcd barrnap/bin./barrnap --help

% barrnap --quiet examples/small.fna##gff-version 3P.marinusbarrnap:0.8rRNA3533143547930+.Name=16S_rRNA;product=16S ribosomal RNAP.marinusbarrnap:0.8rRNA3554643583340+.Name=23S_rRNA;product=23S ribosomal RNAP.marinusbarrnap:0.8rRNA3584333585367.5e-07+.Name=5S_rRNA;product=5S ribosomal RNA% barrnap -q -k mito examples/mitochondria.fna ##gff-version 3AF346967.1barrnap:0.8rRNA6431610.+.Name=12S_rRNA;product=12S ribosomal RNAAF346967.1barrnap:0.8rRNA16723228.+.Name=16S_rRNA;product=16S ribosomal RNA  % barrnap -o rrna.fa < contigs.fa > rrna.gff% head -n 3 rrna.fa>16S_rRNA::gi|329138943|tpg|BK006945.2|:455935-456864(-)ACGGTCGGGGGCATCAGTATTCAATTGTCAGAGGTGAAATTCTTGGATTTATTGAAGACTAACTACTGCGAAAGCATTTGCCAAGGACGTTTTCATTA

• --help show help and exit
• --version print version in formbarrnap X.Y and exit
• --citation print a citation and exit

• --kingdom is the database to use: Bacteria:bac, Archaea:arc, Eukaryota:euk, Metazoan Mitochondria:mito
• --threads is how many CPUs to assign tonhmmer search
• --evalue is the cut-off fornhmmer reporting, before further scrutiny
• --lencutoff is the proportion of the full length that qualifies aspartial match
• --reject will not include hits below this proportion of the expected length

• --quiet will not print any messages tostderr
• --incseq will include the full input sequences in the output GFF
• --outseq creates a FASTA file with the hit sequences

Barrnap does not do anything fancy. It has HMM models for each different rRNA gene.They are built from full length seed alignments.

Barrnap is designed to be a substitute forRNAmmer.It was motivated by my desire to removeProkka'sdependency on RNAmmer which is encumbered by a free-for-academic sign-uplicense, and by RNAmmer's dependence on legacy HMMER 2.x which conflictswith HMMER 3.x that most people are using now.

RNAmmer is more sophisticated than Barrnap, and more accurate because ituses HMMER 2.x in glocal alignment mode whereas NHMMER 3.x currently onlysupports local alignment (Sean Eddy expected glocal to be supported in 2014,but it still isn't available in 2018).

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 willprobably miss wierd rRNAs. The HMM models it uses are derived from Rfam,Silva and RefSeq.

Bacteria (70S)          LSU 50S                5S      RF00001                23S     SILVA-LSU-Bac        SSU 30S                16S     RF00177Archaea (70S)           LSU 50S                5S      RF00001                5.8S    RF00002                23S     SILVA-LSU-Arc        SSU 30S                16S     RF01959Eukarya (80S)           LSU 60S                5S      RF00001                5.8S    RF00002                28S     SILVA-LSU-Euk        SSU 40S                18S     RF01960Metazoan Mito                12S     RefSeq (MT-RNR1, s-rRNA, rns)                16S     RefSeq (MT-RNR2, l-rRNA, rnl)

Fungi[Sajeet Haridas]        LSU 35S ?                5S                5.8S                25S        SSU ?                18S        Mito [http://www.ncbi.nlm.nih.gov/nuccore/NC_001224.1]                15S                 21S (multiple exons)                Apicoplast [http://www.ncbi.nlm.nih.gov/nuccore/U87145.2]                LSU ~2500bp 28S ?                SSU ~1500bp 16S ?Plant [Shaun Jackman]Mito [https://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=26556996]5S~118 bp  ?rrn5 (use RF00001 ?)18S~1935 bp ?rrn18(use RF01960 ?)26S~2568 bp ?rrn26

The name Barrnap was originally derived fromBacterial/Archaeal Ribosomal RNA Predictor.However it has since been extended to support mitochondrial and eukaryotic rRNAs, and has beengiven the new backronymBAsic Rapid Ribosomal RNA Predictor.The project was originally spawned at CodeFest 2013 in Berlin, Germanyby Torsten Seemann and Tim Booth.

• Barrnap:GPLv3
• Rfam:CC0
• SILVA:Free for academic use

Torsten Seemann