<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>Not really, but the functional annotation tools included with maker might be useful for some of the downstream work. Although I guess there is a way I could fool maker's direct protein2genome gene creation into generating gene models with a little code modification.</div><div><br></div><div>--Carson</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> Shane Brubaker <<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 31 July, 2012 1:17 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<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> RE: [maker-devel] CDS file?<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 14 (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"><span style="color:#1F497D">One more question – do people ever run MAKER on transcriptomes?<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in"><p class="MsoNormal"><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "> Carson Holt [<a href="mailto:carsonhh@gmail.com">mailto:carsonhh@gmail.com</a>]
<br><b>Sent:</b> Tuesday, July 31, 2012 6:01 AM<br><b>To:</b> Shane Brubaker; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] CDS file?<o:p></o:p></span></p></div></div><p class="MsoNormal"><o:p> </o:p></p><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">Use the fasta_tool script that comes with MAKER together with the --trim_maker_utr option.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">Thanks,<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">Carson<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in"><p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Shane Brubaker <<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>><br><b>Date: </b>Monday, 30 July, 2012 7:52 PM<br><b>To: </b>"<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><b>Subject: </b>[maker-devel] CDS file?<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p></div><div><div><p class="MsoNormal"><span style="color:black">Hi, does anyone know if maker outputs a file of just the CDS portion of transcripts? I want to use it to determine a codon usage table.<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">Thanks,<o:p></o:p></span></p><p class="MsoNormal"><span style="color:black">Shane<o:p></o:p></span></p></div></div><p class="MsoNormal"><span style="font-size:10.5pt;color:black">_______________________________________________ maker-devel mailing list
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