[Bioperl-l] parsing KGML files

anupam sinha anupam.contact at gmail.com
Wed May 27 01:27:02 EDT 2009


Dear all,
             I am working on evolutionary dynamics of protein interaction
networks for which I need enzyme-centric metabolic networks(i.e nodes in
this network consists of enzymes and they are connected if the product of
one is a substrate of other and/or they share a common metabolite). How can
I parse KGML (KEGG XML) files to extract information in above mentioned
format????
For example....


Source_node       Destination node

enzyme1             enzyme2
enzyme3             enzyme5
enzyme6             enzyme8

enzyme1 interacts with enzyme2 because the product of the reaction catalysed
by enzyme1 happens to be the substrate for enzyme2 etc.

Any help will be appreciated.

Thanks and Regards,

Anupam Sinha,
Graduate Student,
Centre for DNA Fingerprinting and Diagnostics,
Hyderabad, India-500001


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