[maker-devel] CDS retrieve from augustus_masked

[Carson Holt]

It's all CDS, from start to finish.  There is never any UTR in the ab initio
reference match/match_part alignments.  There are two reasons for this.
First most ab initio predictors don't produce UTR.  Second GFF3 has n
is_analysis flag, so it is impossible to separate final gene models from
predicted gene models if they are both in the form gene/mRNA/exon/CDS.
Augustus can predict UTR, but gien the limitation just mentioned, if I
reject the model, I have to trim it before adding it to the reference
information.

We've actually been in discussion with the apollo development group over
this limitation.  Original apollo found the same limitation, so they make
the same assumption for loading data into the browsing window
(gene/mRNA/exon/CDS features always go in the middle annotation track and
everything else goes in the reference evidence track).  With the new web
apollo, we're working on getting the default behavior to allow UTR in the
gene predictions by using the SO predicted gene term in the GFF3 (which
previously wasn't available for use in apollo and maker).

So in summary. Nothing but CDS form now, but will include CDS when available
in the sequence in the near future.

Thanks,
Carson


From:  "Kang, Yang Jae" <kangyangjae at gmail.com>
Date:  Saturday, 6 April, 2013 7:24 AM
To:  'Michael Thon' <mike.thon at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] CDS retrieve from augustus_masked

Thank for your quick response Mike
I looked the file named transcript, but it might include UTRs I suspect.
What I want to do is calculating Ka Ks values so that I need coding
sequences. Is there any indication where is exact START and STOP in the
transcript file? 
 
Thank you
 
 

From: Michael Thon [mailto:mike.thon at gmail.com]
Sent: Saturday, April 06, 2013 8:20 PM
To: Kang, Yang Jae
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] CDS retrieve from augustus_masked
 
Hi Kang - After running fasta_merge there should be a file:

 

[prefix].all.maker.augustus_masked.transcripts.fasta

 

in the output directory.  Is that what you need?

Mike

 

On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <kangyangjae at gmail.com> wrote:


Dear everyone!
 
I want to retrieve CDS sequences from the output of maker; however, in the
augustus_masked feature there is no indication of CDS or Exon like maker
features. Is there any way for me to retrieve CDS from augustus_masked?
There were protein sequences in outdir but no CDS information.
 
Thank you!
 
Kang, Yang Jae
Ph.D.
Cropgenomics Lab.
College of Agriculture and Life Science
Seoul National University
Korea
 
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