[maker-devel] Use pass-through system to add missing genes

[Daniel Hughes]

For cross-species comparisons you might have be better off including the
actual peptide sequences of the other fungi too in the annotation run - I'd
be very surprised if you really did get the same result.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> I  have a set of predicted proteins from the genome of a fungus annotated
> by MAKER  using EST data from a closely related species and 3 ab initio
> predictors  (snap iterativelly trained 3 times, genemark trained directly
> on the assembly and augustus with a model from a less closely related
> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
> when I compare to the species i used EST data from, and there is good
> evidence from alignments that these genes exist. The question is how to
> proceed from Blast hits to actual gene models here. The idea would be to
> add these genes to the existing dataset, rather than reannotate the genome.
> I believe that reannotating it without any further evidence such as RNA-seq
> from the species itself would not change much,and i d rather stick with
> actual predictions that i trust and have used in subsequent analyses. The
> 1000 genes I can accept to annotate with a less stringent and reliable way
> than MAKER, I just want to add them so that the difference in gene count
> gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the
> legacy annotations scheme to do it, by providing GFF3 of the alignments
> between the two species in the regions where genes were missed, but as i
> said, I would not like to reannotate the whole genome, and running MAKER2
> might cause slight changes that i d like to avoid. Is this possible? First,
> is it possible to provide a Gff3 file of specific locations and not the
> entire genome alignment? (I guess so..) Second, how can I tag the existing
> annotations as 'not to be changed' or alternatively, tag the new models
> only? How should I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
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