Question: KEGG database query
0
gravatar for sharmatina189059
9 weeks ago by
United States
sharmatina18905910 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 • 183 views
ADD COMMENTlink modified 9 weeks ago by Pierre Lindenbaum102k • written 9 weeks ago by sharmatina18905910
0
gravatar for Pierre Lindenbaum
9 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum102k 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 9 weeks ago by Pierre Lindenbaum102k

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 9 weeks ago by sharmatina18905910

And why single KO ID gives multiple pathway name?

ADD REPLYlink written 9 weeks ago by sharmatina18905910
cat yourfile | while read A ; do wget ....

??

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Pierre Lindenbaum102k

Really thanks it works..thankyou so much

ADD REPLYlink written 9 weeks ago by sharmatina18905910
1

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

ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum102k
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