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News: J-Express 2011 released. Download from jexpress.bioinfo.no
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Author Topic: Import KEGG pathways, ftp url incorrect  (Read 6335 times)
Chris Fenton
Posts: 1

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« on: April 02, 2008, 01:43:20 PM »

Tried importing KEGG Vibrio fisheria or vfi from methods->pathway analysis without success.

Pressing download set fails probably because the ftp address in incorrect.
The application is searching ftp.genome.ad.jp/pub/pathways which does not exist.
The link is now http://ftp://ftp.genome.jp/pub/kegg/pathway/  or http://ftp://ftp.genome.jp/pub/kegg/pathway/organisms.

So I tried downloading the entire KEGG vfi directory into ..\J-Express Pro 2.7\resources\PW directory.
Vfi then appeared in the pathway look up in the right hand pane under downloaded sets.
But unfortunately it did not appear in the Kegg Pathways pathway set drop down box.
Meaning I could not select vfi as an option.

Is there something obvious I am missing, or ?

Bjarte Dysvik
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Posts: 117

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« Reply #1 on: April 03, 2008, 10:28:06 AM »

As long as it appears under downloaded sets it should be available in the drop down box. I think I remember that we had to make some changes to the Kegg reader in version 2.8 to adjust for format changes, but I need to check this.

Thanks for the new ftp locations.

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