[maker-devel] Serious Start Codon Problem

[Carson Holt]

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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> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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