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Download genes from KEGG pathway

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?

r python
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updated by theobroma22 theobroma22 • written by User000 User000

2 answers

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.

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written by Whoknows Whoknows

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.

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written by theobroma22 theobroma22

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

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written by User000 User000

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.

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written by theobroma22 theobroma22

thanks a lot! i will have a look!

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written by User000 User000

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