Native R Implementation of an Efficient BLAST-Like Algorithm

Implementation of an efficient BLAST-like sequence comparison algorithm, written in 'C++11' and using native R datatypes. Blaster is based on 'nsearch' - Schmid et al (2018) .

Blaster

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.

Installation

From Conda

conda install -c conda-forge r-blaster 

Development version from GitHub

devtools::install_github("tamminenlab/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")

Tested on

• linux_64, r-base >= 4.0, r-cpp >= 1.0.5
• osx_64, r-base >= 4.0, r-cpp >= 1.0.5
• win_64, r-base >= 4.0, r-cpp >= 1.0.5

Details available at https://anaconda.org/conda-forge/r-blaster/files.