<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; ">It's all CDS, from start to finish. There is never any UTR in the ab initio reference match/match_part alignments. There are two reasons for this. First most ab initio predictors don't produce UTR. Second GFF3 has n is_analysis flag, so it is impossible to separate final gene models from predicted gene models if they are both in the form gene/mRNA/exon/CDS. Augustus can predict UTR, but gien the limitation just mentioned, if I reject the model, I have to trim it before adding it to the reference information.</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">We've actually been in discussion with the apollo development group over this limitation. Original apollo found the same limitation, so they make the same assumption for loading data into the browsing window (gene/mRNA/exon/CDS features always go in the middle annotation track and everything else goes in the reference evidence track). With the new web apollo, we're working on getting the default behavior to allow UTR in the gene predictions by using the SO <span style="color: rgb(0, 0, 0); font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; font-family: Verdana, Arial, Helvetica, sans-serif; ">predicted gene term in the GFF3 (which previously wasn't available for use in apollo and maker).</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span style="color: rgb(0, 0, 0); font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; font-family: Verdana, Arial, Helvetica, sans-serif; "><br></span></div><div style="text-align: left; "><font class="Apple-style-span" face="Verdana,Arial,Helvetica,sans-serif"><span class="Apple-style-span" style="font-size: 12px;">So in summary. Nothing but CDS form now, but will include CDS when available in the sequence in the near future.</span></font></div><div style="text-align: left; "><font class="Apple-style-span" face="Verdana,Arial,Helvetica,sans-serif"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div><div style="text-align: left; "><font class="Apple-style-span" face="Verdana,Arial,Helvetica,sans-serif"><span class="Apple-style-span" style="font-size: 12px;">Thanks,</span></font></div><div style="text-align: left; "><font class="Apple-style-span" face="Verdana,Arial,Helvetica,sans-serif"><span class="Apple-style-span" style="font-size: 12px;">Carson</span></font></div><div style="text-align: left; "><font class="Apple-style-span" face="Verdana,Arial,Helvetica,sans-serif"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><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> "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com">kangyangjae@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Saturday, 6 April, 2013 7:24 AM<br><span style="font-weight:bold">To: </span> 'Michael Thon' <<a href="mailto:mike.thon@gmail.com">mike.thon@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<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 retrieve from augustus_masked<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=utf-8"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><base href="x-msg://15/"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="KO" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; ">Thank for your quick response Mike<o:p></o:p></span></p><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; ">I looked the file named transcript, but it might include UTRs I suspect. What I want to do is calculating Ka Ks values so that I need coding sequences. Is there any indication where is exact START and STOP in the transcript file? <o:p></o:p></span></p><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; "><o:p> </o:p></span></p><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; ">Thank you<o:p></o:p></span></p><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; "><o:p> </o:p></span></p><p class="MsoNormal" style="word-break:break-hangul"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: '?? ??'; "><o:p> </o:p></span></p><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "> Michael Thon [<a href="mailto:mike.thon@gmail.com">mailto:mike.thon@gmail.com</a>] <br><b>Sent:</b> Saturday, April 06, 2013 8:20 PM<br><b>To:</b> Kang, Yang Jae<br><b>Cc:</b> <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] CDS retrieve from augustus_masked<o:p></o:p></span></p></div></div><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p><p class="MsoNormal"><span lang="EN-US">Hi Kang - After running fasta_merge there should be a file:<o:p></o:p></span></p><div><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span lang="EN-US">[prefix].all.maker.augustus_masked.transcripts.fasta<o:p></o:p></span></p><div><div><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span lang="EN-US">in the output directory. Is that what you need?<o:p></o:p></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Mike<o:p></o:p></span></p></div><div><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span lang="EN-US">On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com">kangyangjae@gmail.com</a>> wrote:<o:p></o:p></span></p></div><p class="MsoNormal"><span lang="EN-US"><br><br><o:p></o:p></span></p><div><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Dear everyone!<o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; "><o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">I want to retrieve CDS sequences from the output of maker; however, in the augustus_masked feature there is no indication of CDS or Exon like maker features. Is there any way for me to retrieve CDS from augustus_masked? There were protein sequences in outdir but no CDS information.<o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; "><o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Thank you!<o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; "><o:p></o:p></span></p><p class="MsoNormal"><b><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Kang, Yang Jae</span></b><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; "><o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Ph.D.<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Cropgenomics Lab.<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">College of Agriculture and Life Science<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Seoul National University<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; ">Korea<o:p></o:p></span></p><p class="MsoNormal" style="text-align:justify;text-justify:inter-ideograph"><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: ????, serif; "><o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size: 13.5pt; font-family: Helvetica, sans-serif; ">_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com"><span style="color:purple">maker-devel@box290.bluehost.com</span></a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org"><span style="color:purple">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</span></a><o:p></o:p></span></p></div></div><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p></div></div></div></div>_______________________________________________
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