[maker-devel] tRNAscan GFF3

[Carson Holt]

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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