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</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:"Malgun Gothic";color:#1F497D'>Thank you for quick response again! <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:"Malgun Gothic";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:"Malgun Gothic";color:#1F497D'>I found the non-ATG starting sequences in transcript file. I thought this would be the UTR traces, and I additionally found the offset value some position after ‘>’ letter. Is that indicate the starting ATG?<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:"Malgun Gothic";color:#1F497D'>Secondly, there is several files named *.augustus_masked.proteins.fasta, *.non_overlapping_ab_initio.proteins.fasta, and *.proteins.fasta. What is the criteria of splitting those files? The reason why I’m asking is that some genes were redundant between *.augustus_masked.proteins.fasta and *.proteins.fasta.<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:"Malgun Gothic";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:"Malgun Gothic";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:"Malgun Gothic";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"'> Carson Holt [mailto:carsonhh@gmail.com] <br><b>Sent:</b> Sunday, April 07, 2013 12:13 AM<br><b>To:</b> Michael Thon; 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><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'>Augustus only predicts UTR for a handful of organisms. I trim them off the rejected models before outputting to the GFF3 as match/match_part features (per my previous e-mail concerning the limitations of GFF3).<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'> --Carson<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'><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:11.0pt;font-family:"Calibri","sans-serif";color:black'>From: </span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Michael Thon <<a href="mailto:mike.thon@gmail.com">mike.thon@gmail.com</a>><br><b>Date: </b>Saturday, 6 April, 2013 10:37 AM<br><b>To: </b>"Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com">kangyangjae@gmail.com</a>><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 style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'>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...<o:p></o:p></span></p><div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'>On Apr 6, 2013, at 1:24 PM, "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 style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'><br><br><o:p></o:p></span></p><div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";color:#1F497D'>Thank for your quick response Mike</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";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?</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";color:#1F497D'> </span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";color:#1F497D'>Thank you</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";color:#1F497D'> </span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Malgun Gothic";color:#1F497D'> </span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> </span></span><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Michael Thon [<a href="mailto:mike.thon@">mailto:mike.thon@</a><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</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span lang=EN-US style='color:black'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='color:black'>Hi Kang - After running fasta_merge there should be a file:<o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'>[prefix].all.maker.augustus_masked.transcripts.fasta<o:p></o:p></span></p></div><div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'>in the output directory. Is that what you need?<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'>Mike<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='color:black'>On Apr 6, 2013, at 9:25 AM, "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com"><span style='color:purple'>kangyangjae@gmail.com</span></a>> wrote:<o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=EN-US style='color:black'><br><br><br><o:p></o:p></span></p></div><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";color:black'>Dear everyone!</span><span lang=EN-US style='color:black'><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";color:black'> </span><span lang=EN-US style='color:black'><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";color:black'>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.</span><span lang=EN-US style='color:black'><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";color:black'> </span><span lang=EN-US style='color:black'><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";color:black'>Thank you!</span><span lang=EN-US style='color:black'><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";color:black'> </span><span lang=EN-US style='color:black'><o:p></o:p></span></p><div><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>Kang, Yang Jae</span></b><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>Ph.D.</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>Cropgenomics Lab.</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>College of Agriculture and Life Science</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>Seoul National University</span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"맑은고딕","serif";color:black'>Korea</span><span lang=EN-US style='color:black'><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:"Helvetica","sans-serif";color:black'> </span><span lang=EN-US style='color:black'><o:p></o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>_______________________________________________<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></span><span lang=EN-US style='color:black'><o:p></o:p></span></p></div></div></div></div></div></div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div></div><p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:black'>_______________________________________________ maker-devel mailing list <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a> <a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a> <o:p></o:p></span></p></div></body></html>