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<p class="MsoNormal">If you have a fairly recent version of Bioperl (now at 1.7.1) this should not be an issue within bioperl (note this isn’t a bug per se, just that the default universal codon table has rare codons so we simply added a ‘strict’ alternative
table). <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Also, based on that thread Carson also added a workaround in MAKER explicitly setting a ‘strict’ codon table that should be in 3.00.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Nathan Ricks <nathan.ricks@gmail.com><br>
<b>Date: </b>Wednesday, August 2, 2017 at 9:54 PM<br>
<b>To: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>[maker-devel] (no subject)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">As I have been submitting my genome sequences to NCBI, I've come to realise that about 1/10 of the transcripts generated have an incorrect start codon. When I look at the genes manually, they usually have a start codon 3 or 6 base pairs
away. What could be causing this?<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I read about a previous issue where there was a mistake in Bioperl and the fix was implemented many version ago. I have maker version 3.00<br>
<br>
<a href="https://groups.google.com/forum/#!searchin/maker-devel/start$20codon|sort:relevance/maker-devel/S0j1fJ4LjVY/5ugSG01kKkUJ">https://groups.google.com/forum/#!searchin/maker-devel/start$20codon|sort:relevance/maker-devel/S0j1fJ4LjVY/5ugSG01kKkUJ</a><o:p></o:p></p>
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