[maker-devel] Serious Start Codon Problem

[JH Gmail]

Slightly off-topic questions:  What is the assessment of right and wrong based on? Is there a training set based on experiments? In bacteria, the use of the minor starts is significant, but the mechanism is so different I would expect eukaryotes to be more strict. 

Does maker handle ribosome profiling yet?

jim

Sent from my iPad

> On Oct 24, 2013, at 8:55 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> 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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