<html 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"><head><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><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:굴림;
panose-1:2 11 6 0 0 1 1 1 1 1;}
@font-face
{font-family:굴림;
panose-1:2 11 6 0 0 1 1 1 1 1;}
@font-face
{font-family:"맑은 고딕";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@맑은 고딕";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:"\@굴림";
panose-1:2 11 6 0 0 1 1 1 1 1;}
@font-face
{font-family:맑은고딕;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"\@맑은고딕";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:굴림;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"맑은 고딕";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:3.0cm 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=KO link=blue vlink=purple><div class=WordSection1><p class=MsoNormal style='word-break:break-hangul'><span lang=EN-US style='font-size:10.0pt;font-family:"맑은 고딕";color:#1F497D'>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:10.0pt;font-family:"맑은 고딕";color:#1F497D'>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:10.0pt;font-family:"맑은 고딕";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='word-break:break-hangul'><span lang=EN-US style='font-size:10.0pt;font-family:"맑은 고딕";color:#1F497D'>Thank you<o:p></o:p></span></p><p class=MsoNormal style='word-break:break-hangul'><span lang=EN-US style='font-size:10.0pt;font-family:"맑은 고딕";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='word-break:break-hangul'><span lang=EN-US style='font-size:10.0pt;font-family:"맑은 고딕";color:#1F497D'><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:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Michael Thon [mailto:mike.thon@gmail.com] <br><b>Sent:</b> Saturday, April 06, 2013 8:20 PM<br><b>To:</b> Kang, Yang Jae<br><b>Cc:</b> maker-devel@yandell-lab.org<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:10.0pt;font-family:"맑은고딕","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:10.0pt;font-family:"Helvetica","sans-serif"'> </span><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","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:10.0pt;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></p><p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span lang=EN-US style='font-size:10.0pt;font-family:"Helvetica","sans-serif"'> </span><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","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:10.0pt;font-family:"맑은고딕","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:10.0pt;font-family:"Helvetica","sans-serif"'> </span><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'><o:p></o:p></span></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'>Kang, Yang Jae</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'>Ph.D.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'>Cropgenomics Lab.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'>College of Agriculture and Life Science<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif"'>Seoul National University<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","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:10.0pt;font-family:"Helvetica","sans-serif"'> </span><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","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></body></html>