README.md

R-CMD-check CRAN status

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.

Installation

# Install release version from CRAN
install.packages("blaster")

# Install development version from GitHub
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")



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blaster documentation built on Oct. 27, 2021, 5:08 p.m.