KEGG Reconstruct Pathway: More Efficient Usage

Hi,

I have a list of ~4000 genes and their associated KO number. Currently they're in the following format:

Gene1 K09806

Gene2 K09806

...

I'm hoping to find a program that annotates each KO with all associated pathways in the following format:

Gene1 K09806 (Pathways associated with KO)

Gene2 K09201 (Pathways associated with KO)

...

Looking into Kegg's Reconstruct Pathway program: http://www.kegg.jp/kegg/tool/map_pathway.html, the function to annotate all pathways is present. However, the output format is a messy html page. Are there any other tools available?

Thanks!

kegg pathway genome

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updated 5.4 years ago by Biostar

• written 9.0 years ago by taylrtam •

1 answer

Have a go at the KEGGREST package available on Bioconductor for R.

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written 9.0 years ago by theobroma22

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