How barrnap predicts ribosomal RNA on the genome
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RNAmmer, a rRNA forecasting software, is available for free only to users of universities and scientific research institutions. In the spirit of open source, a scientific research team developed barrnap, which is completely open source and free. The github link is as follows
Https://github.com/tseemann/barrnap
The software supports the following types of rRNA predictions
Bacteria (5SMagne23SMagol 16s)
Archaea (5S, 5.8S, 23S, 16s)
Metazoan mitochondria (12Spar 16s)
Eukaryotes (5S, 5.8S, 28S, 18s)
Compared with RNAmmer, the rRNA prediction of mitochondria is added in addition to the basic bacteria, archaea and eukaryotes.
The software is developed in Perl language and depends on nhmmer and bedtools. The installation process is as follows
Git clone https://github.com/tseemann/barrnap
Download the source code locally through git, which is the executable program in the bin directory. It is important to make sure that the nhmmer and bedtools software are installed and that the corresponding paths are added to the PATH environment variable.
The basic usage of the software is as follows
Barrnap-- kingdom bac-- threads 8-- quiet small.fna > rRNA.gff3
-- kingdom parameter specifies the species type. Bac represents bacteria, arc represents Archaea, euk represents eukaryotes, mito represents metazoan mitochondria;-- threads specifies the number of parallel threads.
The prediction results are saved in GFF3 format. Examples are as follows
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