<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Correct. Current MAKER 2.31.9 AND 3.00 beta have the strict codon table workaround for BioPerl.<div class=""><br class=""></div><div class="">MAKER’s default behavior is to use the same ORF given to it be the predictor and alter start codon if MAKER itself is able to add extra sequence that can extend the ORF during the UTR addition phase and find a start codon. But if you set alway_complete=1 in the options, it will walk upstream and downstream to find start/stop codons in the surrounding sequence even if it has to add sequence to the exons.<br class=""><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 3, 2017, at 9:14 AM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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). <span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">chris<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel-bounces@yandell-lab.org</a>> on behalf of Nathan Ricks <<a href="mailto:nathan.ricks@gmail.com" style="color: purple; text-decoration: underline;" class="">nathan.ricks@gmail.com</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Wednesday, August 2, 2017 at 9:54 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[maker-devel] (no subject)<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div><p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 11pt; font-family: Calibri, sans-serif;">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 class=""><br class=""><a href="https://groups.google.com/forum/#!searchin/maker-devel/start$20codon|sort:relevance/maker-devel/S0j1fJ4LjVY/5ugSG01kKkUJ" style="color: purple; text-decoration: underline;" class="">https://groups.google.com/forum/#!searchin/maker-devel/start$20codon|sort:relevance/maker-devel/S0j1fJ4LjVY/5ugSG01kKkUJ</a><o:p class=""></o:p></p></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">maker-devel@box290.bluehost.com</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""></div></blockquote></div><br class=""></div></div></body></html>