Question: KEGG database query
0
gravatar for sharmatina189059
20 months ago by
United States
sharmatina18905930 wrote:

Dear all I have 1900 KEGG KO Ids like K03821, k21699 and so on . I have retrieved it for my genome using BLASTKoala. I want to retrieve corresponding pathway name, substrate, product, enzyme name, enzyme class, interacting pathways, reaction type and source.

please let me know how to use kegg api for this purpose or using some per or bioperl code.

kegg database query • 732 views
ADD COMMENTlink modified 20 months ago by Pierre Lindenbaum120k • written 20 months ago by sharmatina18905930
0
gravatar for Pierre Lindenbaum
20 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

using togogws:

 for A in K03821 K21699 ; do wget -q -O - "http://togows.org/entry/kegg-orthology/${A}/pathways" | sed "s/\$/ ${A}/" ; done

ko00650  Butanoate metabolism K03821
ADD COMMENTlink written 20 months ago by Pierre Lindenbaum120k

Thanks for sending your reply. It really works but what if I have a file of 1900 KO. How to use multiple KO for this purpose.

ADD REPLYlink written 20 months ago by sharmatina18905930

And why single KO ID gives multiple pathway name?

ADD REPLYlink written 20 months ago by sharmatina18905930
cat yourfile | while read A ; do wget ....

??

ADD REPLYlink modified 20 months ago • written 20 months ago by Pierre Lindenbaum120k

Really thanks it works..thankyou so much

ADD REPLYlink written 20 months ago by sharmatina18905930
1

Click on the pale green check mark on the left to validate+close please.

ADD REPLYlink written 20 months ago by Pierre Lindenbaum120k
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