<div dir="ltr">Hi,<br><br>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<br>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Nov 3, 2013 at 7:16 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.<div>
<br></div><div>
Thanks,</div><div>Carson</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Oct 24, 2013 at 7:42 AM, graham etherington (TSL) <span dir="ltr"><<a href="mailto:graham.etherington@sainsbury-laboratory.ac.uk" target="_blank">graham.etherington@sainsbury-laboratory.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
I notice that the latest version of Maker available from<br>
<a href="http://www.yandell-lab.org/software/maker.html" target="_blank">http://www.yandell-lab.org/software/maker.html</a> is still v2.29b (4 Oct<br>
2013). As we're also having the start codon problem we'd like to get hold<br>
of v2.30. Do you know when this will be released?<br>
Many thanks,<br>
Graham<br>
<br>
<br>
Dr. Graham Etherington<br>
Bioinformatics Support Officer,<br>
The Sainsbury Laboratory,<br>
Norwich Research Park,<br>
Norwich NR4 7UH.<br>
UK<br>
Tel: <a href="tel:%2B44%20%280%291603%20450601" value="+441603450601" target="_blank">+44 (0)1603 450601</a><br>
<br>
<br>
<br>
<br>
<br>
On 13/10/2013 06:26, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<br>
<br>
>Before Wednesday, because after that I'm on a 6 day road trip, so I have<br>
>to have it wrapped up before I leave.<br>
><br>
>--Carson<br>
><br>
><br>
><br>
><br>
>On 10/12/13 12:16 PM, "Felix Bemm" <<a href="mailto:felix.bemm@uni-wuerzburg.de" target="_blank">felix.bemm@uni-wuerzburg.de</a>> wrote:<br>
><br>
>>Thx Carson! Do you now when 2.30 will be available? Bests<br>
>><br>
>>On 12.10.2013 17:48, Carson Holt wrote:<br>
>>> This issue just came up this week on another e-mail as well.<br>
>>><br>
>>> One way to fix it, is to edit the Bio::Tools::CodonTable module from<br>
>>> BioPerl (use maker --debug to have maker print out the locations of all<br>
>>> modules it uses). Such a hack should only be done as a temporary work<br>
>>> around.<br>
>>><br>
>>> You change line 256 from --><br>
>>> ---M---------------M---------------M----------------------------<br>
>>><br>
>>> To--><br>
>>> -----------------------------------M----------------------------<br>
>>><br>
>>><br>
>>> Maker uses the BioPerl is_start_codon function to determine if the<br>
>>>codon<br>
>>> used in a result it receives is acceptable or if it should look<br>
>>>upstream<br>
>>> or downstream for a different one. Apparently there are actually 3<br>
>>> acceptable start codons in the standard codon table (2 rare ones and<br>
>>>one<br>
>>> common), so making the edit removes the two rare ones from the list.<br>
>>><br>
>>> I'm also preparing a 2.30 release that exports a "strict" codon table<br>
>>>to<br>
>>> the BioPerl module, that will be used by default and should fix the<br>
>>>issue.<br>
>>><br>
>>> Thanks,<br>
>>> Carson<br>
>>><br>
>>><br>
>>><br>
>>> On 10/12/13 11:06 AM, "Felix Bemm" <<a href="mailto:felix.bemm@uni-wuerzburg.de" target="_blank">felix.bemm@uni-wuerzburg.de</a>> wrote:<br>
>>><br>
>>>> Hi,<br>
>>>><br>
>>>> I have a serious problems with maker annotations especially the start<br>
>>>> codon placement. It started happening with maker version 2.27! About<br>
>>>>1/3<br>
>>>> of my genes are missing a proper start codon. When reviewing the GFF<br>
>>>> files gene predictors and est evidence standalone would predict the<br>
>>>> right gene structure including the start codon. I was thinking that<br>
>>>>this<br>
>>>> problem was somehow linked to my gene models but looking at their<br>
>>>> standalone prediction I discarded that theory. Just some stats about<br>
>>>> proteins with proper start codon (first column) and missing start<br>
>>>>codon<br>
>>>> (second column).<br>
>>>><br>
>>>> Maker 9268 4215<br>
>>>> SNAP 16577 896<br>
>>>> Genemark 18764 290<br>
>>>><br>
>>>> Numbers look the same when Augustus is used (currently retraining).<br>
>>>> Manually using EST's in Apollo often fixes the problems but I don't<br>
>>>>want<br>
>>>> to check > 4000 genes for this.<br>
>>>><br>
>>>> Do you have any idea what could cause such a problem? If you need some<br>
>>>> example gff files I can send you.<br>
>>>><br>
>>>> Best regards<br>
>>>> Felix<br>
>>>><br>
>>>> --<br>
>>>> Felix Bemm<br>
>>>> Department of Bioinformatics<br>
>>>> University of Würzburg, Germany<br>
>>>> Tel: <a href="tel:%2B49%20931%20-%2031%2083696" value="+499313183696" target="_blank">+49 931 - 31 83696</a><br>
>>>> Fax: <a href="tel:%2B49%20931%20-%2031%2084552" value="+499313184552" target="_blank">+49 931 - 31 84552</a><br>
>>>> <a href="mailto:felix.bemm@uni-wuerzburg.de" target="_blank">felix.bemm@uni-wuerzburg.de</a><br>
>>>><br>
>>>> _______________________________________________<br>
>>>> maker-devel mailing list<br>
>>>> <a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
>>>><br>
>>>><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br>
>><br>
>>--<br>
>>Felix Bemm<br>
>>Department of Bioinformatics<br>
>>University of Würzburg, Germany<br>
>>Tel: <a href="tel:%2B49%20931%20-%2031%2083696" value="+499313183696" target="_blank">+49 931 - 31 83696</a><br>
>>Fax: <a href="tel:%2B49%20931%20-%2031%2084552" value="+499313184552" target="_blank">+49 931 - 31 84552</a><br>
>><a href="mailto:felix.bemm@uni-wuerzburg.de" target="_blank">felix.bemm@uni-wuerzburg.de</a><br>
><br>
><br>
><br>
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