[maker-devel] Serious Start Codon Problem

[Fields, Christopher J]

Done, with some added tests.  I labeled it 'Strict' ('Canonical' can be a bit of a loaded term).  It's currently set as ID 24.

I will likely push out a new 1.6 point release this week or next, I'll merge these in for that release.

chris

On Oct 14, 2013, at 12:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think adding one more codon table to the set of available tables would
> be sufficient.  Call it the 'Strict' table or 'Canonical' table.  It
> doesn't need to be the default, but should be a selectable option just as
> the other codon tables are.  There is a way to export codon tables to the
> module, which is what I've now added to MAKER, but I'm sure other BoiPerl
> users would find a strictly canonical codon table useful as well.
> 
> Thanks,
> Carson
> 
> 
> On 10/14/13 11:07 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> 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
>>>>>> 
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> 
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>> 
>>>> -- 
>>>> 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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>> 
> 
>