[maker-devel] Serious Start Codon Problem

[Mark Yandell]

Hi Graham,

 Carson is currently on the road, moving his family from Canada back to the States. He should be back online sometime next week. Sorry for the delay.


--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of graham etherington (TSL) [graham.etherington at sainsbury-laboratory.ac.uk]
Sent: Thursday, October 24, 2013 7:42 AM
To: Carson Holt; Felix Bemm; maker-devel at yandell-lab.org
Cc: Kate Bailey (TSL)
Subject: Re: [maker-devel] Serious Start Codon Problem

Hi,
I notice that the latest version of Maker available from
http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
2013). As we're also having the start codon problem we'd like to get hold
of v2.30. Do you know when this will be released?
Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:

>Before Wednesday, because after that I'm on a 6 day road trip, so I have
>to have it wrapped up before I leave.
>
>--Carson
>
>
>
>
>On 10/12/13 12:16 PM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>
>>Thx Carson! Do you now when 2.30 will be available? Bests
>>
>>On 12.10.2013 17:48, Carson Holt wrote:
>>> This issue just came up this week on another e-mail as well.
>>>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from
>>> BioPerl (use maker --debug to have maker print out the locations of all
>>> modules it uses).  Such a hack should only be done as a temporary work
>>> around.
>>>
>>> You change line 256 from -->
>>> ---M---------------M---------------M----------------------------
>>>
>>> To-->
>>> -----------------------------------M----------------------------
>>>
>>>
>>> Maker uses the BioPerl is_start_codon function to determine if the
>>>codon
>>> used in a result it receives is acceptable or if it should look
>>>upstream
>>> or downstream for a different one. Apparently there are actually 3
>>> acceptable start codons in the standard codon table (2 rare ones and
>>>one
>>> common), so making the edit removes the two rare ones from the list.
>>>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table
>>>to
>>> the BioPerl module, that will be used by default and should fix the
>>>issue.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a serious problems with maker annotations especially the start
>>>> codon placement. It started happening with maker version 2.27! About
>>>>1/3
>>>> of my genes are missing a proper start codon. When reviewing the GFF
>>>> files gene predictors and est evidence standalone would predict the
>>>> right gene structure including the start codon. I was thinking that
>>>>this
>>>> problem was somehow linked to my gene models but looking at their
>>>> standalone prediction I discarded that theory. Just some stats about
>>>> proteins with proper start codon (first column) and missing start
>>>>codon
>>>> (second column).
>>>>
>>>> Maker              9268    4215
>>>> SNAP               16577   896
>>>> Genemark   18764   290
>>>>
>>>> Numbers look the same when Augustus is used (currently retraining).
>>>> Manually using EST's in Apollo often fixes the problems but I don't
>>>>want
>>>> to check > 4000 genes for this.
>>>>
>>>> Do you have any idea what could cause such a problem? If you need some
>>>> example gff files I can send you.
>>>>
>>>> Best regards
>>>> Felix
>>>>
>>>> --
>>>> Felix Bemm
>>>> Department of Bioinformatics
>>>> University of Würzburg, Germany
>>>> Tel: +49 931 - 31 83696
>>>> Fax: +49 931 - 31 84552
>>>> felix.bemm at uni-wuerzburg.de
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>>
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>--
>>Felix Bemm
>>Department of Bioinformatics
>>University of Würzburg, Germany
>>Tel: +49 931 - 31 83696
>>Fax: +49 931 - 31 84552
>>felix.bemm at uni-wuerzburg.de
>
>
>
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