[maker-devel] Maker not outputting exons with EST and Protein Evidence

[Innocent Onsongo]

Thanks for the insight.


On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> This is because augustus never calls it either without hints or after
> being given hints by MAKER.  This may be because even though the exon has
> support from ESTs and protein alignments, it breaks the open reading frame
> (you can check using apollo – just click and drag them into the annotation
> tier).  I did this individually for each of the polished proteins and ESTs,
> and none have proper open reading frame.
>
> Perhaps the official annotation contains a frame shift or something to
> make it work (augustus can't do that).  Such a thing is not all that
> uncommon.  There are many instances of RefSeq annotations for example where
> if you cut out the exons and try and translate them, they won't translate.
>  This can happen because the reference sequence changed or is incorrect,
> and if the annotation was generated from a different assembly, then it just
> gets mapped as best as possible to the current assembly and the correct
> protein translation is saved elsewhere in the database (even though manual
> translation won't directly reproduce it).  Genes where this happens make up
> just under 1% of the human genome (but they can drive you nuts especially
> if your analysis expects protein sequence to match the nucleotide sequence
> translation).  It's really just an artifacts of the process used to move
> annotations forward on the humans genome every time they update the
> assembly.
>
> Thanks,
> Carson
>
>
> From: Innocent Onsongo <onson001 at umn.edu>
> Date: Monday, July 8, 2013 6:12 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker not outputting exons with EST and Protein
> Evidence
>
> Maker Developers,
>
> I am testing Maker on a well annotated contig from the encode project and
> in one of the genes, maker does not output an exon despite HSPs supporting
> it. I have attached a compressed folder with
>
> ENr122_genes.gff: The validated genes as per encode
> ENr122.gff: Makers output
> maker_opts.ctl: The control file I used
> ENr122_98669-134249.pptx: A power point visually illustrated the exon in
> question.
>
> I even set the parameters est2genome and protein2genome to 1 but still
> Maker did not output this exon.
>
> Is there a good reason Maker does no have this exon in its final model
> despite the HSPs supporting it?
>
> Thanks,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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