[maker-devel] Can maker select a gene model based on #algoritham predicted it

[Carson Holt]

It's not an option in exactly the way you are specifying, but there is
something I usually do for annotation that works well.  I run interproscan
or rpsblast on the non_overlapping.proteins.fasta file and select just
those non-overlapping models that have a recognizable protein domain (just
searching the pfam doamin space is more than sufficient).  Then I provide
the selected results to model_gff, and provide the previous maker results
to the maker_gff option with (all reannotation pass options set to 1 and
all analysis options turned off).  This adds models with at least
recognizable domains (as even multiple gene predictors can overpredict in
a similar way).

Attached is a script to help select predictions and upgrade them to models
in GFF3 format.  If you have question let me know.

Thanks,
Carson



On 12-05-29 5:54 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>Thanks for all the help during the long weekend, in spite of that long
>drive. I am still trying to imagine that.
>
>I now have maker to consider our own prediction via pred_gff, and use
>augustus and gene mark (with our training model). And i was able to use
>altest and protein evidences. Maker happily picks one gene model when
>there is a overlap between three different predictions. But, when I look
>at the gff, it seems like it picks a gene model only when there is an
>est/protein evidence. It leaves out some genes even though, they are
>predicted by all three algorithms. Of course, keep_pred=1 helps to keep
>all the models. This kind of leads to over prediction.
>
>But, I am looking for something in between. And would like to know if
>that is possible?
>1) Pick a gene model if it has an evidence from (est/prot etc...)
>irrespective of how many algorithms predicted it
>2) In the absence of extrinsic evidence (est/prot etc), pick a gene model
>if that is predicted by at least two algorithms.
>
>Or even simpler:
>I have ab-initio predictions from three algorithms, Can I output, those
>genes that is supported by at least two of them. I care less about
>exactness of gene boundaries.
>
>Thanks,
>Gowthaman
>
>PS: With my recent attempts, i learned couple things about maker/other
>associated tools that is not documented in gmod-maker wiki. Is it
>possible/ok if I add contents to it. I am okay with running it by you
>before making it public.

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