README.md

In guokai8/seq2Fun: Annotate sequences with KEGG pathways

seq2Fun

seq2Fun provides function to annotate protein or coding sequences with KEGG pathways

Description

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+ and diamond software.

Requirement

The blast+ or diamond should be installed before installing seq2Fun package

Installation

library(devtools)
install_github("guokai8/seq2Fun")

Software Usage

library(seq2Fun)
## check if blast+ or diamond 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, set runblast = FALSE if you prefer diamond
seqs <- db$db[sample(500, 10)] ## random choose 10 sequences
ann <- seq2fun(query = seqs, db = db, type = "blastp", evalue = 1e-10, num_threads = 2)
## set bidirectional = TRUE if you prefer bidirectional blast
## set runblast = FALSE if you prefer diamond
head(ann)

Note

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).

Contact information

For any questions please contact [e-mail]

guokai8/seq2Fun documentation built on March 22, 2020, 8:10 p.m.