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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.