rblast

Workflows

Create Custom Blast Db

Create a custom BLAST database from user-provided sequences and query it locally.

library(rBLAST)
library(Biostrings)
# Load example sequences
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta", package = "rBLAST"))
# Write to FASTA
writeXStringSet(seq, filepath = "seqs.fasta")
# Create database
makeblastdb("seqs.fasta", db_name = "db/small", dbtype = "nucl")

Note: Input is an XStringSet object, and output is a set of local BLAST database files written to disk.

Standard Workflow

Download, extract, and query an existing NCBI BLAST database using local BLAST.

library(rBLAST)
# Download and extract 16S database
tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
untar(tgz_file, exdir = "16S_rRNA_DB")

# Load existing database
bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")

# Query database
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta", package = "rBLAST"))[1]
cl <- predict(bl, seq)

Note: Input is a path to a local BLAST database and a query XStringSet object; output is a data.frame of matches.

Create And Query Custom Db

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data

library(rBLAST)
library(Biostrings)
# 1. Read reference sequences
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta", package = "rBLAST"))
# 2. Write sequences to a FASTA file
writeXStringSet(seq, filepath = "seqs.fasta")
# 3. Create custom BLAST database
makeblastdb("seqs.fasta", db_name = "db/small", dbtype = "nucl")
# 4. Load custom database
db <- blast("db/small")
# 5. Extract a subsequence fragment
fragment <- subseq(seq[1], start = 101, end = 200)
# 6. Query custom database
res <- predict(db, fragment)

Note: Input is a set of reference sequences and a query fragment; output is a data.frame of alignment matches.