<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 style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="color: rgb(31, 73, 125); font-size: 13px; font-family: 'Malgun Gothic'; ">I additionally found the offset value some position after ‘>’ letter. Is that indicate the starting ATG?</span></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Only in the maker.transcripts.fasta will have offsets other than 0, you can use these to get the transcription offset. All other *.transcript.fasta files will always have an offset of 0 for the reason previously mentioned. Some genes will not start with ATG or have stop codons. These are partial models. Set always_complete=1 to reduce these.</div></blockquote><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><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"><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: 'Malgun Gothic'; "><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: 'Malgun Gothic'; ">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?</span></p></div></div></div></span><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Final selected annotations go in the maker.proteins.fasta and maker.transcripts.fasta files. Raw unfiltered ab initio prediction from augustus go in the augustus_masked.proteins.fasta and augustus_masked.transcripts.fasta file (these are for reference purposes). A set of non-redundant rejected models go in the non-overlapping.transcripts.fasta and non-overlapping.proteins.fasta files (if you are missing a gene you expected to find, look in this file first – you can add them back if you find protein domains in them for example).</div></blockquote><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><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"><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: 'Malgun Gothic'; ">The reason why I’m asking is that some genes were redundant between *.augustus_masked.proteins.fasta and *.proteins.fasta.</span></p></div></div></div></span><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">This is because some of the augustus generated models made it into the final annotation set.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div></blockquote><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION"><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"><div lang="KO" link="blue" vlink="purple"><div class="WordSection1"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><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; "> Carson Holt [<a href="mailto:carsonhh@gmail.com">mailto:carsonhh@gmail.com</a>] <br><b>Sent:</b> Sunday, April 07, 2013 12:13 AM<br><b>To:</b> Michael Thon; 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" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><span lang="EN-US"><o:p> </o:p></span></p><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; ">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 style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; "><o:p> </o:p></span></p></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; "> --Carson<o:p></o:p></span></p></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; "><o:p> </o:p></span></p></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><p class="MsoNormal"><b><span lang="EN-US" style="font-size: 11pt; color: black; font-family: Calibri, sans-serif; ">From: </span></b><span lang="EN-US" style="font-size: 11pt; color: black; font-family: Calibri, sans-serif; ">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 style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; "><o:p> </o:p></span></p></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><div><p class="MsoNormal"><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; ">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; color: black; font-family: Calibri, sans-serif; ">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; color: black; font-family: Calibri, sans-serif; "><br><br><o:p></o:p></span></p><div><div><p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; ">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: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; ">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: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; "> </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: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; ">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: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; "> </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: 10pt; color: rgb(31, 73, 125); font-family: 'Malgun Gothic'; "> </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: 10pt; color: black; font-family: Tahoma, sans-serif; ">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 10pt; color: black; font-family: Tahoma, sans-serif; "> </span></span><span lang="EN-US" style="font-size: 10pt; color: black; font-family: Tahoma, sans-serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: Helvetica, sans-serif; "> </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: 10pt; color: black; 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.</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: 10pt; color: black; font-family: Helvetica, sans-serif; "> </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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: Helvetica, sans-serif; "> </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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: ????, serif; ">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: 10pt; color: black; font-family: Helvetica, sans-serif; "> </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; color: black; 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></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; color: black; font-family: Calibri, sans-serif; "><o:p> </o:p></span></p></div></div><p class="MsoNormal" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; "><span lang="EN-US" style="font-size: 10.5pt; color: black; font-family: Calibri, sans-serif; ">_______________________________________________ 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></div></div></span></body></html>