KEGG Reconstruct Pathway: More Efficient Usage
1
0
Entering edit mode
3.8 years ago
taylrtam • 0

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 • 1.7k views
ADD COMMENT
0
Entering edit mode
3.8 years ago
theobroma22 ★ 1.1k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1605 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6