Blaster implements an efficient BLAST-like sequence comparison algorithm, written in C++11 and using native R datatypes. Blaster is light-weight, fast and dependency-free. The code base of Blaster is adapted from nsearch. An implementation of nsearch for Python is available at npysearch.
conda install -c conda-forge r-blaster devtools::install_github("tamminenlab/blaster")# Read a query file into DataFrame
query <- read_fasta("inst/extdata/query.fasta")
# Read a database file into a DataFrame
db <- read_fasta("inst/extdata/db.fasta")
# BLAST the query against the database
blast_table <-
blast(query, db)
# BLAST protein sequence file against itself using filenames as blast function arguments
prot_blast_table <-
blast(query = "inst/extdata/prot.fasta",
db = "inst/extdata/prot.fasta",
alphabet = "protein")
# Filter the sequences containing motif GAGACTT
query <- read_fasta("query.fasta", "GAGACTT")Details available at https://anaconda.org/conda-forge/r-blaster/files.