Question: download KEGG genes sequence in fasta format
1
gravatar for Dattatray Mongad
16 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad330 wrote:

Is there any tool or script or package to download the KEGG gene sequence in fasta format by KO ids? I have list of KO's.

kegg sequence gene genome • 630 views
ADD COMMENTlink written 16 months ago by Dattatray Mongad330

It would help if you post some example KOs here. Use keggrest and user manual here. Sequence object is biostrings. You can write them to hdd in fasta format using biostrings package (writeXStringSet function). Try below example code and example kegg IDs are taken from manual::

library(KEGGREST)
test.seq=keggGet(c("hsa:10458", "ece:Z5100"), "ntseq")
library(Biostrings)
writeXStringSet(test.seq,"temp.fa", format = "fasta")
ADD REPLYlink modified 16 months ago • written 16 months ago by cpad011212k
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