[maker-devel] CDS retrieve from augustus_masked

Sat Apr 6 12:45:02 MDT 2013

Thank you for quick response again! 

I found the non-ATG starting sequences in transcript file. I thought this
would be the UTR traces, and I additionally found the offset value some
position after '>' letter. Is that indicate the starting ATG?

Secondly, there is several files named *.augustus_masked.proteins.fasta,
*.non_overlapping_ab_initio.proteins.fasta, and *.proteins.fasta. What is
the criteria of splitting those files? The reason why I'm asking is that
some genes were redundant between *.augustus_masked.proteins.fasta and
*.proteins.fasta.

Thank you

From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Sunday, April 07, 2013 12:13 AM
To: Michael Thon; Kang, Yang Jae
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] CDS retrieve from augustus_masked

Augustus only predicts UTR for a handful of organisms.  I trim them off the
rejected models before outputting to the GFF3 as match/match_part features
(per my previous e-mail concerning the limitations of GFF3).

 --Carson

From: Michael Thon <mike.thon at gmail.com>
Date: Saturday, 6 April, 2013 10:37 AM
To: "Kang, Yang Jae" <kangyangjae at gmail.com>
Cc: <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] CDS retrieve from augustus_masked

Thats a good point because 'transcripts' implies that it would have the
UTRs. Does augustus predict the UTRs?  I manually checked the translations
of the .transcript. file and I only found valid translations but that does
not mean that UTRs could not be present...

On Apr 6, 2013, at 1:24 PM, "Kang, Yang Jae" <kangyangjae at gmail.com> wrote:

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" <
<mailto:kangyangjae at gmail.com> 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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