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

[Hung-Wei Hsu]

Thanks a lot for your helps.
Your suggestions will be greatly helpful for our analysis.

I've tried to add EST sequences to improve gene predictions.
The EST sequences I used were CDS sequences of the same organism.
But I got an error as below.

substr outside of string at .../TranslationMachine.pm line 162
ERROR: Failed while polishig ESTs
ERROR: Chunk failed at level:2, tier_type:3

What's wrong with my analysis?
The EST sequences I used are wrong?
Thank you.

Hung-Wei



2013/5/21 Carson Holt <carsonhh at gmail.com>

> 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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