Blaster - a native R implementation of an efficient BLAST-like algorithm

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.

Installation

# install.packages("devtools")
devtools::install_github("manutamminen/blaster")

Examples

# 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")