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

[Carson Holt]

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
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