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

Tue May 22 07:14:17 MDT 2012

Hi again,
I hav sent an email a few days ago about this thread, and i am not  
sure if you have received it or you still did not have time to look at  
it. In any case, this email was dealing with the fact that some  
proteins were not retrieved in the abinitio models and how to deal  
with it. What I would like to ask here is a few confirmations on how  
to rerun maker for the proteins that were retrieved in the abinitio  
models. i have looked at the Blast results, and have done a series of  
check-ups, so now I am ready to run MAKER again with a list of models  
that I want to retain.
Regarding the following parameters:

1. Do I  set the genome= to nothing here? i.e quote it out? This is in  
the beginning of the control file
#-----Genome (Required for De-Novo Annotation)
genome=#genome sequence file in fasta format
organism_type= #eukaryotic or prokaryotic. Default is eukaryotic

>
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
>
> #-----Gene Prediction
2. Do i provide again the snap etc models? I am not sure, because i  
thought MAKER would not run ab initio predictors this time (this is  
why I would also quote out the genome file above, as this is not a de  
novo annotation). but if it will, i will then provide the previous  
models i used, except for snap, for which I will generate a new model   
from the gff3 file of the last run (according to snap documentation).  
Am i correct?
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
>
> keep_preds=1

Samely, what do i do with repeatmasking etc?
Thanks in adavance,
Anastasia

>
> Barry
>
>>> Thanks,
>>> Carson
>>>
>>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>>> To: <maker-devel at yandell-lab.org>
>>> Subject: [maker-devel] Use pass-through system to add missing genes
>>>
>>> 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
>>> <gff3_select>
>>
>> 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
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
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> lab.org

Anastasia (Natassa) Gioti
Post-Doc Researcher
Evolutionary Biology Department Uppsala University -Science for Life  
lab, Karolinska Institute Stockholm
anastasia.gioti at ebc.uu.se
anastasia.gioti at scilifelab.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/