<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>It's a naming issue. The reference match/match_part features have 'abinit' in the name while the non-overlapping fasta file has 'processed' in the name of the fasta header. The easiest way to fix it is to just replaced 'processed' with 'abinit' in the terms you are searching for. This was supposed to be resolved already, but I'll see what's going on. What version of MAKER are you using?</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Mack, Brian" <<a href="mailto:Brian.Mack@ARS.USDA.GOV">Brian.Mack@ARS.USDA.GOV</a>><br><span style="font-weight:bold">Date: </span> Monday, September 8, 2014 at 7:47 AM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] non-overlapping predictions<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 12 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal">Hi,<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">I used IPRscan on the non-overlapping ab initio proteins and identified additional predictions that I want to include in my final gff. I was trying to follow the advice given in this thread (<a href="http://gmod.827538.n3.nabble.com/Adding-non-overlapping-models-to-final-set-td4043778.html">http://gmod.827538.n3.nabble.com/Adding-non-overlapping-models-to-final-set-td4043778.html</a>)
to pull out these predictions from the full Maker gff3 that includes all the evidence, but it seems that none of the non-overlapping predictions are in this gff3 file. Where would I find all of the predictions including the non-overlapping predictions?<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Thanks,<o:p></o:p></p><p class="MsoNormal">Brian<o:p></o:p></p></div><br><br><br><br>
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