Download genes from KEGG pathway

Question

[User000]

Hello,

I am would like to download all genes of i.e. arabidopsis thaliana from i.e. circadian rhythm pathway in fasta format. Is there a way to download them in a batch mode, instead of opening and saving every single gene in a fasta format?

[farzaneafzali]

You can use download section of wikipathways to download all the pathways in your preferred organism: https://www.wikipathways.org/index.php/Download_Pathways

Answer 1

[Whoknows]

Hi

Some part of KEGG is not free anymore but your could try this link for downloading free section of the database.

You could also search your genes in UniProt and find their relevant pathways in mapping section.

Answer 2

[theobroma22]

Each KEGG pathway's KGML file should contain all the associated Entrez IDs. This way you wouldn't need the sequences, but are easily accessible if you should require them.

[User000]

thank you, I have KGML files, but I am interested in having the seq-s...how can I download them? (not 1 by 1..)

[theobroma22]

There are many ways to do this...One way is to use the keggGet function in the KEGGREST package available on Bioconductor. There is a limitation to the number of IDs you can search at one time so you will need to make a simple for loop to iterate over the vector of your circadian rhythm NCBI Entrez IDs. I haven't used it in a very long time but try the plant BiomaRt database online or R package for which Arabidopsis is available.

[User000]

thanks a lot! i will have a look!