[maker-devel] gene duplicates and track the query protein

[Carson Holt]

2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein?
Not directly.  Proteins can align to multiple locations, so you will get more than one protein overlapping a gene.  A reciprocal BLAST would probably be the best thing to do here.  If the MAKER derived annotation, and a gene are both each others best hit in separate blast jobs, then you could usually safely call them the same gene.  You would have to do that outside of MAKER.

Thanks,
Carson


From: Barry Moore <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>
Date: Thursday, 6 September, 2012 12:35 PM
To: Zhou Qi <muntjaczhou at gmail.com<mailto:muntjaczhou at gmail.com>>
Cc: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] gene duplicates and track the query protein


On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote:

Dear maker users and developers:

I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions:

1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication?

MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP).  If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci.


2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein?


I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here?


B

I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways?

Many thanks!

Qi
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
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