<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"><base href="x-msg://15/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thats a good point because 'transcripts' implies that it would have the UTRs. Does augustus predict the UTRs? I manually checked the translations of the .transcript. file and I only found valid translations but that does not mean that UTRs could not be present...<br><div><div>On Apr 6, 2013, at 1:24 PM, "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com">kangyangjae@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="KO" link="blue" vlink="purple" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); ">Thank for your quick response Mike<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); ">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></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); ">Thank you<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: '맑은 고딕'; color: rgb(31, 73, 125); "> </span></div><div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm; "><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><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; "><span class="Apple-converted-space"> </span>Michael Thon [mailto:mike.thon@<a href="http://gmail.com">gmail.com</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Saturday, April 06, 2013 8:20 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Kang, Yang Jae<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] CDS retrieve from augustus_masked<o:p></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US">Hi Kang - After running fasta_merge there should be a file:<o:p></o:p></span></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"> </span></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US">[prefix].all.maker.augustus_masked.transcripts.fasta<o:p></o:p></span></div><div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"> </span></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US">in the output directory. Is that what you need?<o:p></o:p></span></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US">Mike<o:p></o:p></span></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"> </span></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US">On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com" style="color: purple; text-decoration: underline; ">kangyangjae@gmail.com</a>> wrote:<o:p></o:p></span></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"><br><br><o:p></o:p></span></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Dear everyone!<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; "><o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, 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></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; "><o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Thank you!<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; "><o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><b><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Kang, Yang Jae</span></b><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; "><o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Ph.D.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Cropgenomics Lab.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">College of Agriculture and Life Science<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Seoul National University<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; ">Korea<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; text-align: justify; "><span lang="EN-US" style="font-size: 10pt; font-family: Helvetica, sans-serif; "> </span><span lang="EN-US" style="font-size: 10pt; font-family: 맑은고딕, serif; "><o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><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" style="color: purple; text-decoration: underline; "><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" style="color: purple; text-decoration: underline; "><span style="color: purple; ">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</span></a><o:p></o:p></span></div></div></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 굴림; "><span lang="EN-US"></span></p></div></div></div></blockquote></div><br></body></html>