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

[Anastasia Gioti]

Hi, 
Do you mean that I should have not include the proteins of the closely related species in my fungal protein fasta file that I used as evidence in MAKER? i do not see why... What I have been trying to do now is further 'bias' the annotations in favor of this species, so as to get the missing genes. Can you explain a bit more whta you mean?
Thanks, 
Anastasia
On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:

> 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/
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 

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/



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20120425/c9541b0c/attachment-0003.html>