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<div class="">On May 18, 2019, at 10:10 PM, Carson Hinton Holt <<a href="mailto:carson.holt@genetics.utah.edu" class="">carson.holt@genetics.utah.edu</a>> wrote:</div>
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Hi Samia,
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<div class="">I’ve CC’d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it’s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are
interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes.</div>
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<div class="">Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission.</div>
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<div class="">—Carson</div>
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<div class="">On May 17, 2019, at 2:30 AM, djerroud samia <<a href="mailto:djerroudsamia@gmail.com" class="">djerroudsamia@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hello,
<div class="">thank you for your answer, I suscribed to the mailing list, but seems that it will take a little time. My question is quite urgent. IF you can answer to my answers from here it would be cool.</div>
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<div class="">Well, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that:</div>
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<div class=""> gene 478..1299</div>
<div class=""> /locus_tag="DU99_RS00005"</div>
<div class=""> /old_locus_tag="DU99_00005"</div>
<div class=""> CDS 478..1299</div>
<div class=""> /locus_tag="DU99_RS00005"</div>
<div class=""> /old_locus_tag="DU99_00005"</div>
<div class=""> /function="miscellaneous; hypothetical/global homology"</div>
<div class=""> /inference="COORDINATES: similar to AA</div>
<div class=""> sequence:RefSeq:NP_384107.1"</div>
<div class=""> /note="Derived by automated computational analysis using</div>
<div class=""> gene prediction method: Protein Homology."</div>
<div class=""> /codon_start=1</div>
<div class=""> /transl_table=11</div>
<div class=""> /product="phosphoenolpyruvate synthase regulatory protein"</div>
<div class=""> /protein_id="WP_010968285.1"</div>
<div class=""> /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL</div>
<div class=""> IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS</div>
<div class=""> YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT</div>
<div class=""> PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT</div>
<div class=""> QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR"</div>
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<div class="">Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :)</div>
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<div class="">Thank you,</div>
<div class="">Samia</div>
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<div dir="ltr" class="gmail_attr">Le jeu. 16 mai 2019 à 14:25, Carson Hinton Holt <<a href="mailto:carson.holt@genetics.utah.edu" class="">carson.holt@genetics.utah.edu</a>> a écrit :<br class="">
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<div style="overflow-wrap: break-word;" class="">You can post error to the MAKER devel mailing list —> <a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank" class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a>
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<div class="">You can search for previous posts to the devel list here (FYI, the google group used is an archive, you must still post original questions to the list above) —> <a href="http://groups.google.com/group/maker-devel" target="_blank" class="">http://groups.google.com/group/maker-devel</a></div>
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<div class="">Also general info is at wiki here —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page" target="_blank" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page</a></div>
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<div class="">—Carson</div>
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<div class="">On May 16, 2019, at 7:13 AM, djerroud samia <<a href="mailto:djerroudsamia@gmail.com" target="_blank" class="">djerroudsamia@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hello,
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<div class="">I am very new in using maker, I get some errors. can you tell me who is the person who deals with the technical problems of maker</div>
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<div class="">Thank you,</div>
<div class="">Samia</div>
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