[maker-devel] Serious Start Codon Problem

[Carson Holt]

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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>