[maker-devel] Serious Start Codon Problem

[Janna Fierst]

Hi,

I can't get my message to post to the list but I had a problem with
2.29-beta in parallel - it seemed to restart the same scaffolds over and
over instead of moving on to a new set. I was running the same as the 2.28
version, is it something with our mpi system here at UO? Thanks -Janna
Fierst


On Sun, Nov 3, 2013 at 7:16 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 2.30 beta is now available for use.  Sorry about the delay, between moving
> and getting seriously ill for several days, I sort of dropped off the grid
> for 2 weeks.  Give this version a try.
>
> Thanks,
> Carson
>
>
>
>
> On Thu, Oct 24, 2013 at 7:42 AM, graham etherington (TSL) <
> graham.etherington at sainsbury-laboratory.ac.uk> wrote:
>
>> Hi,
>> I notice that the latest version of Maker available from
>> http://www.yandell-lab.org/software/maker.html is still v2.29b (4 Oct
>> 2013). As we're also having the start codon problem we'd like to get hold
>> of v2.30. Do you know when this will be released?
>> Many thanks,
>> Graham
>>
>>
>> Dr. Graham Etherington
>> Bioinformatics Support Officer,
>> The Sainsbury Laboratory,
>> Norwich Research Park,
>> Norwich NR4 7UH.
>> UK
>> Tel: +44 (0)1603 450601
>>
>>
>>
>>
>>
>> On 13/10/2013 06:26, "Carson Holt" <carsonhh at gmail.com> wrote:
>>
>> >Before Wednesday, because after that I'm on a 6 day road trip, so I have
>> >to have it wrapped up before I leave.
>> >
>> >--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.org
>> >>
>> >>--
>> >>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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>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
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