[maker-devel] Serious Start Codon Problem

[Felix Bemm]

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