[maker-devel] Annotations from protein alignments

[Carson Holt]

I updated the 2.31 tar ball.  Go ahead and download it again.
protein2genome was turned off for eukaryotes and only working for
prokaryotic genomes.

—Carson


On 2/12/14, 1:34 AM, "Marc P. Hoeppner" <marc.hoeppner at imbim.uu.se> wrote:

>Dear list,
>
>I have an annotation project with both protein data (it's a bird, so
>I've been using both vertebrates in general and chicken in specific),
>and huge amounts of somewhat dodgy (as in lot's of pre-mRNA) RNA-seq
>data. The chicken augustus model seems to do a decent job in seeding
>gene loci, but it's not quite perfect. I want to use protein alignments
>to create a high-confidence set of exons and subsequently a set of gene
>loci to train e.g. snap), but when testing to set protein2genome=1 I
>never get any annotations. This is also true for the test data set that
>is delivered together with Maker (hsap_). Anything I should know about
>the use of proteins to generate annotations? I left all settings in the
>config file at their defaults (except protein2genome=1). I've tried this
>with both Maker 2.30 and 2.31.
>
>All the best,
>
>Marc
>
>-- 
>-----------
>Marc P. Hoeppner, PhD
>Group leader
>BILS Genome annotation platform
>
>Department of Medical Biochemistry and Microbiology
>Uppsala University, Sweden
>marc.hoepner at imbim.uu.se
>
>
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