[maker-devel] Serious Start Codon Problem

[Carson Holt]

Thanks!!

--Carson


On 10/14/13 2:51 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>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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>>>> 
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>>> 
>> 
>> 
>