KEGG Reconstruct Pathway: More Efficient Usage

Question

[taylrtam]

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!

Answer 1

[theobroma22]

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