[maker-devel] Serious Start Codon Problem

Thu Oct 24 15:09:20 MDT 2013

Hi Jim,

You can and any kind of evidence you want to MAKER including ribosomal profiling data as long as you format it in GFF3 format.  You could pass in your GFF3 formatted ribosomal profiling data in maker_opt.ctl with the protein_gff option and it will be treated as protein evidence.  However if you are wondering if anyone has coded a specific addition to MAKER to accept ribosomal profiling data and treat it as a different kind of evidence then no, this hasn't been done.

B

On Oct 24, 2013, at 8:32 AM, JH Gmail wrote:

> 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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>> 
>> 
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> 
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543

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