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bioguo edited this page Apr 26, 2019
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seq2Fun provides function to annotate protein or coding sequences with KEGG pathways
Annotate the protein and coding sequences with KEGG pathways could be done with KAAS website. Here the seq2Fun try to do same thing with blast function.
The blast+ should be installed before installing seq2Fun package
library(devtools)
install_github("guokai8/seq2Fun")
library(seq2Fun)
## check if blast tools have been installed
blast_help()
head(listspecies)
###Find the correct species name
db <- preparedb(species = "Arabidopsis thaliana", seqtype = "AA", savedb = TRUE)
## Take several minutes
str(db, 2)
###savedb will write out the sequences file in the work directory
makeblastdb(db, dbtype = "prot")
###make blast db
seqs <- db$db[sample(500, 10)] ## random choose 10 sequences
ann <- seq2fun(query = seqs, db = db, evalue = 1e-10, num_threads = 2)
## set bidirectional = TRUE if you prefer bidirectional blast
head(ann)
The seq2Fun downloads and uses KEGG data. Non-academic uses may require a KEGG license agreement (details at http://www.kegg.jp/kegg/legal.html).
For any questions please contact [email protected]