Question: how to grab all kegg organisms having a certain KO eg K15864
0
gravatar for George
22 months ago by
George0
George0 wrote:

Hi,

I'd like to grab the taxonomy of all Kegg organisms having K15864.

I used Download htext, but got everything both organism having and not having K15864.

Any ideas, what to do?

Thanks, George

ADD COMMENTlink modified 22 months ago by theobroma221.1k • written 22 months ago by George0
0
gravatar for theobroma22
22 months ago by
theobroma221.1k
theobroma221.1k wrote:

This is hard because it's not as simple as only having K15864 to do your search; the structure is typically the organism code then the pathway code like hsa : 15864 for human pathways, ece : 15864 for E. coli pathways, etc. I had a look at the KEGGREST package and there might be a way to do it, but with no simple solution or capacity. So, try here: http://www.genome.jp/kegg-bin/show_module?M00175

Click on the reference module for the drop down organism list.

Update: if you click on the Taxonomy tab, it will populate the list and highlight the organisms with that pathway. It shouldn't take you that long to copy and paste them...

ADD COMMENTlink modified 22 months ago • written 22 months ago by theobroma221.1k
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