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.
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.
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