[maker-devel] Mapping gene names

[Sajeet Haridas]

My brief test of barrnap suggests that it does not perform well on rRNA
genes with introns such as those found in fungal mitochondria. Setting a
lower threshold for --reject and --evalue helps, but is not enough.
Looks like I cannot abandon rnammer for now.
FYI - if you want to test barrnap with fungal mitochondria, use --kingdom
bacteria because they have 23S and 16S unlike the human mitochondria.

Sajeet


On Wed, May 14, 2014 at 8:23 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

>  \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>
> 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 --help output seems to be out of date.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/ <http://www.bioinformatics.net.au/>*
>
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