Question: KEGG database query
0
gravatar for sharmatina189059
8 days ago by
United States
sharmatina1890590 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 • 119 views
ADD COMMENTlink modified 8 days ago by Pierre Lindenbaum99k • written 8 days ago by sharmatina1890590
0
gravatar for Pierre Lindenbaum
8 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum99k 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 8 days ago by Pierre Lindenbaum99k

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 8 days ago by sharmatina1890590

And why single KO ID gives multiple pathway name?

ADD REPLYlink written 8 days ago by sharmatina1890590
cat yourfile | while read A ; do wget ....

??

ADD REPLYlink modified 8 days ago • written 8 days ago by Pierre Lindenbaum99k

Really thanks it works..thankyou so much

ADD REPLYlink written 8 days ago by sharmatina1890590
1

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

ADD REPLYlink written 8 days ago by Pierre Lindenbaum99k
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