[maker-devel] Why are some complete gene predictions not present in the final results?

[Carson Holt]

On default settings MAKER will only put ab initio predictions that have some
sort of evidence support (EST or protein) in the final gene set.  The
rejected predictions are still in the GFF3 for reference purposes as
match/match_part features, but not as gene/mRNA/exon/CDS features.  So a
lack of evidence might be why it is not there.  You can add all rejected
models that don't overlap an accepted model by setting keep_preds=1 (this
usually brings a lot more into the final gene set than you really want
though (lots of false positives).  But for some organisms like fungi, which
have high gene densities, this approach is relatively safe.

Alternatively the gene is missing because it overlaps another gene model
that was accepted.  MAKER won't allow overlapping models on the same strand
in eukaryotes.  The only way to force that kind of overlap is to give MAKER
the reference models in model_gff and not let it call it's own models (then
maker is really just aligning evidence and scoring the reference models).

One final note.  If there is no evidence supporting the model, and that is
why it is rejected, you can also try adding more evidence to the maker run
or you can consider the possibility that the gene model in the reference is
not real to being with (i.e. a false positive gene model called during the
initial annotation process and not supported by protein or expression data
from any source).

Thanks,
Carson



From:  Hung-Wei Hsu <ares711122 at gmail.com>
Date:  Monday, 20 May, 2013 12:16 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Why are some complete gene predictions not present
in the final results?

Hi MAKER developers,

I was exploiting MAKER to perform gene prediction and annotation on my
contigs.
I used Artemis to examine gff and found some CDS with complete structure
were absent in the final results.
They are really predicted and annotated on the ref genome.
I'm wondering if they were discarded due to overlapping with another CDS.
How can I preserve these CDS?
Thanks a lot in advance.

Hung-Wei
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