Question: download KEGG genes sequence in fasta format
0
gravatar for Dattatray Mongad
9 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad260 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 • 350 views
ADD COMMENTlink written 9 months ago by Dattatray Mongad260

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 9 months ago • written 9 months ago by cpad011211k
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