[maker-devel] Maker errors

[Carson Hinton Holt]

On May 18, 2019, at 10:10 PM, Carson Hinton Holt <carson.holt at genetics.utah.edu<mailto:carson.holt at genetics.utah.edu>> wrote:

Hi Samia,

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.

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.

—Carson


On May 17, 2019, at 2:30 AM, djerroud samia <djerroudsamia at gmail.com<mailto:djerroudsamia at gmail.com>> wrote:

Hello,
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.

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:

 gene            478..1299
                     /locus_tag="DU99_RS00005"
                     /old_locus_tag="DU99_00005"
     CDS             478..1299
                     /locus_tag="DU99_RS00005"
                     /old_locus_tag="DU99_00005"
                     /function="miscellaneous; hypothetical/global homology"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_384107.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoenolpyruvate synthase regulatory protein"
                     /protein_id="WP_010968285.1"
                     /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL
                     IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS
                     YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT
                     PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT
                     QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR"


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 :)

Thank you,
Samia



Le jeu. 16 mai 2019 à 14:25, Carson Hinton Holt <carson.holt at genetics.utah.edu<mailto:carson.holt at genetics.utah.edu>> a écrit :
You can post error to the MAKER devel mailing list —> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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) —> http://groups.google.com/group/maker-devel

Also general info is at wiki here —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page

—Carson



On May 16, 2019, at 7:13 AM, djerroud samia <djerroudsamia at gmail.com<mailto:djerroudsamia at gmail.com>> wrote:

Hello,

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

Thank you,
Samia



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