[maker-devel] tRNAscan GFF3

[Daniel Standage]

This annotation was generated using Maker 2.31.3.


--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University


On Thu, Aug 21, 2014 at 11:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> It should be on the same strand.  Which MAKER version are you using?
>
> --Carson
>
>
> From: Daniel Standage <daniel.standage at gmail.com>
> Date: Thursday, August 21, 2014 at 9:33 AM
> To: Maker Mailing List <maker-devel at yandell-lab.org>
> Subject: [maker-devel] tRNAscan GFF3
>
> Greetings!
>
> I have a quick question about Maker's handling of tRNAscan output,
> particularly tRNAs containing introns. If I haven't missed something, it
> looks like Maker reports the second exon on the opposite strand as the
> first exon, the tRNA feature, and the gene feature? Am I reading this
> correctly?
>
> I don't think this representation makes sense. The second exon is
> complementary to the first (hence the folding), but it is not encoded on or
> transcribed from the opposite strand. Unless I've misunderstood something,
> I would suggest that the correct representation would be to have all
> features on the same strand.
>
> Thanks,
> Daniel
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Computational Genome Science Laboratory
> Indiana University
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