Question: KEGG database query
0
gravatar for sharmatina189059
2.6 years ago by
United States
sharmatina18905940 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 • 990 views
ADD COMMENTlink modified 2.6 years ago by Pierre Lindenbaum128k • written 2.6 years ago by sharmatina18905940
0
gravatar for Pierre Lindenbaum
2.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k 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 2.6 years ago by Pierre Lindenbaum128k

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 2.6 years ago by sharmatina18905940

And why single KO ID gives multiple pathway name?

ADD REPLYlink written 2.6 years ago by sharmatina18905940
cat yourfile | while read A ; do wget ....

??

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Pierre Lindenbaum128k

Really thanks it works..thankyou so much

ADD REPLYlink written 2.6 years ago by sharmatina18905940
1

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

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum128k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1377 users visited in the last hour