I am a newbie in bioinfo. I would like to know how to download all the pathways of an organism from KEGG database using the KEGG API. Initially I had done it using the FTP but now its no more freely available. Please help me with this!
I don't know your informatic skills, but you could start by taking a look at the rather new KEGG rest API.
If your organism is already inside the KEGG database retrieving all its pathways is relatively easy.
Assume your organism is Homo sapiens (Kegg code "hsa"), you just need to open your browser and go to this page (notice the URL).
This example gives you all the pathways AND the human genes associated to them.
To get info about a gene (for instance hsa:10) just go to this page (again, notice how the URL is built).
If your organism is not inside the KEGG database, you first need to annotate it through KAAS, obtain the KO IDs and then do a search like this (note that there is a limit in the number of KO IDs that you can put in a single URL, so maybe you need to perform more than one search).