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.

When to Use

• Local BLAST Queries: Running local BLAST queries directly from R using Bioconductor XStringSet objects (e.g., RNAStringSet, DNAStringSet).
• Custom BLAST Databases: Creating custom BLAST databases from local FASTA files using makeblastdb and querying them locally.
• NCBI Database Downloads: Downloading and caching pre-trained NCBI BLAST databases (e.g., 16S rRNA) using blast_db_get.

When NOT to Use

• Remote NCBI Queries: For running BLAST queries remotely on NCBI servers without local BLAST+ installation (use annotate::blastSequences instead).
• No Local BLAST+ Installation: If the BLAST+ command-line tools are not installed on the system or not in the system PATH.

Data Requirements

• Query sequences as Biostrings::XStringSet objects (e.g., RNAStringSet).
• Reference sequences in FASTA format for database creation.

Key Parameters

• db: Path to the BLAST database in blast().
• db_name: Output path and name prefix for the database in makeblastdb().
• dbtype ("nucl"): Type of database to create ("nucl" or "prot") in makeblastdb().
• BLAST_args: Additional command-line arguments passed to the BLAST executable in predict() (e.g., "-perc_identity 99").
• custom_format: Custom output format string specifying columns to return in predict().

Best Practices

• Verify BLAST+ is installed and accessible in R using has_blast() or Sys.which("blastn").
• Set the system PATH environment variable using Sys.setenv if R cannot find the BLAST+ executables.
• Organize custom database files by specifying a directory prefix (e.g., db/small) in makeblastdb.
• Use unlink with recursive = TRUE to clean up temporary database directories and FASTA files.

Common Pitfalls

• BLAST executable not found: Sys.which("blastn") returns "". Fix: Set the PATH environment variable to include the BLAST+ installation directory.
• Database files missing or corrupted: Occurs if the database path is incorrect. Fix: Ensure the database prefix matches the one specified during makeblastdb.

Alternatives

• annotate: Use blastSequences for querying the remote NCBI BLAST server.

Citations

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology.

References

• Homepage: bioconductor.org/packages/rblast
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/rblast/inst/doc/rblast.html