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Clarify that Barrnap handles metazoan mitochondria #14

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Clarify that Barrnap handles metazoan mitochondria #14

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28 changes: 20 additions & 8 deletions README.md
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Expand Up @@ -10,7 +10,7 @@ Torsten Seemann - torsten.seemann@gmail.com - @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).
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.
Expand Down Expand Up @@ -90,7 +90,7 @@ Eukarya (80S)
28S SILVA-LSU-Euk
SSU 40S
18S RF01960
Mito
Metazoan mitochondria
12S RefSeq (MT-RNR1, s-rRNA, rns)
16S RefSeq (MT-RNR2, l-rRNA, rnl)

Expand All @@ -102,25 +102,37 @@ Fungi
25S
SSU ?
18S
Mito [http://www.ncbi.nlm.nih.gov/nuccore/NC_001224.1]
Fungal mitochondria [http://www.ncbi.nlm.nih.gov/nuccore/NC_001224.1]
15S
21S (multiple exons)


TODO: Shaun Jackman @sjackman
Plantae
Plastid <http://www.ncbi.nlm.nih.gov/nuccore/NC_009618>
LSU
4.5S
5S
23S
SSU
16S
Mitochondria <http://www.ncbi.nlm.nih.gov/nuccore/NC_010303>
LSU
5S
26S
SSU
18S

TODO:
Apicoplast [http://www.ncbi.nlm.nih.gov/nuccore/U87145.2]
LSU ~2500bp 28S ?
SSU ~1500bp 16S ?

Plastid [Shaun Jackman]
?

</pre>

## 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
However it has since been extended to support metazoan 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.
Expand Down