[maker-devel] Serious Start Codon Problem

[Carson Holt]

Probably Tuesday or Wednesday.

--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
>>>
>>> _______________________________________________
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>
>-- 
>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