[maker-devel] Mapping gene names

[Fields, Christopher J]

\o/

(now I can get rid of rnammer forever!)

chris

On May 14, 2014, at 6:33 PM, Torsten Seemann <torsten.seemann at monash.edu<mailto:torsten.seemann at monash.edu>> wrote:

Carson & Shaun

It doesn’t appear to support eukaryotes though.

Barrnap supports bacteria, archaea, mitochondria and eukaryotes. The barrnap --help output seems to be out of date.

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 does support eukaryota and mitochondria, I just forgot to push the documentation changes. This has been resolved now in the 0.4.2 release.

  --kingdom [X]     Kingdom: euk arc bac mito (default 'bac')

Next release 0.5 will have an 'accurate' mode which will fine tune the predictions using cmalign glocal alignment.

Thanks for your interest!

--
--Dr Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University, AUSTRALIA
--Life Sciences Computation Centre, VLSCI, Parkville, AUSTRALIA
--http://www.bioinformatics.net.au/

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