[maker-devel] Maker and mono-exonic genes ?

[Carson Holt]

One more note.  The ESTs appear to be from multiple overlapping HSPs (based
on red line pattern in image).  I'd have to see the actual GFF3 to be sure,
but if that is the case, then there probably isn't an ORF to work with at
that location on that strand (so SNAP can't call it).  Possibly the result
of assembly error or a pseudogene.

--Carson



From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Friday, 7 June, 2013 5:32 PM
To:  Bérénice Benayoun <benayoun at stanford.edu>,
"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Maker and mono-exonic genes ?

Hi Berenice, Thank you for sending that screenshot and the maker_opts.log
file. Those are exactly what we need to understand how to expect MAKER to
perform. 

In looking at the screenshot, it doesn't look like any of the gene
predictors gave a prediction in this region. Uses the predictions from
ab-initio tools as a basis for models and considers models that are
supported by evidence. It won't by default create a model when there isn't a
prediction in the region.

Can I ask which gene predictors you used and how they were trained? You
might consider training one or more of them on the specific evidence that
you expect to support these genes and then rerunning maker with the
retrained predictors.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
Bérénice Benayoun [benayoun at stanford.edu]
Sent: Friday, June 07, 2013 11:17 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] Maker and mono-exonic genes ?

Dear maker developers,

I am currently annotating a de novo fish genome, and have started looking
for genes of interest in particular in Maker's output to verify that it's
outputting proper gene sets.

While many of the genes I look for seem to be correctly annotated by the
pipeline, I have noticed that important genes that do have strong
evidentiary support but are monoexonic are NOT reported by maker.

I am attaching a screenshot for the contig that I know should contain the
Foxl2 gene (notoriously monoexonic across evolution), and highlighted the
corresponding evidence for it.

Is there any setting I can give to maker to force it to output monoexonic
genes ? I already set "single_exon=1" with no success. I attached my config
file FYI.

Thank you so much in advance for your answer !!!

Best,

Berenice.
-- 
Bérénice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
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