[maker-devel] Serious Start Codon Problem

[Fields, Christopher J]

Carson,

Regarding the CodonTable change below, should this be something that needs to be fixed, or made more flexible, in bioperl?  I could see this being a problem if using MAKER for bacterial annotation (where the alternative start codons are actually more common).

chris

On Oct 14, 2013, at 9:45 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
> 
> 
> 
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