how to grab all kegg organisms having a certain KO eg K15864

Question

[George]

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

Answer 1

[theobroma22]

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...