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