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  • maryam
    Junior Member
    • Apr 2013
    • 8

    Please help me with KEGG annotation

    Hi there,

    This is my frist post here, hope to get your help and experience.

    I have done a de novo transcriptome assembly of Illumina PE reads, I then used the KAAS server at http://www.genome.jp/kaas-bin/kaas_main for KEGG annotation of my assembly. It assigned the KO numbers to the related contigs and showed the pathway, where the EC number of enzymes involved in the various reactions illustrated and the existing ortholog (contigs) colored in green, however, there is no information which contigs involved in the given pathway. I would like to know how I can view these genes (contigs) in the various steps of a given pathway. For a better explanation of my issue, I attached the TCA pathway generated by KEGG as an example, please take a look at it. As you better know me, those genes (from my gene list) that are available in the pathway, colored in the green box. I want to know which gene(s) has corresponded to each green box.
    I also contacted with the KEGG support for this question and they told me "We provide xml files if you are good at programming. You may be able to find the coordinates of boxes on a map. http://www.kegg.jp/kegg/xml/". Unfortunately, I could not find a solution there as I'm a beginner in this field. I would be highly appreciated for hearing any help and suggestion from you in this regard.
    Attached Files
  • SylvainL
    Senior Member
    • Feb 2012
    • 180

    #2
    Actually, they are right. All the informations you are looking for are in the xml files. You can parse them (using R for example) to have the information you are looking for in a table...

    Comment

    • maryam
      Junior Member
      • Apr 2013
      • 8

      #3
      Thank you Sylvainl, Could you please advise me to use R or any tool to get the information, actually which gene(s) has corresponded to each green box in the pathway? It will be great if there is any tutorial or documentation for this task as I'm really new in this field.

      Comment

      • SylvainL
        Senior Member
        • Feb 2012
        • 180

        #4
        You can parse with the XML package (function xmlParse) and then work with list (xmlToList)...

        Comment

        • maryam
          Junior Member
          • Apr 2013
          • 8

          #5
          Thank you very much, however, I need more help, something like a step-by-step guide as I'm totally blind here.

          Comment

          • SylvainL
            Senior Member
            • Feb 2012
            • 180

            #6
            You can start by looking here...

            Comment

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