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# R package rBLAST - R Interface for the Basic Local Alignment Search Tool
[](https://mhahsler.r-universe.dev/rBLAST)
[](https://bioconductor.org/packages/rBLAST)
Interfaces the Basic Local Alignment Search Tool (BLAST) to search
genetic sequence data bases with the Bioconductor infrastructure. This
includes interfaces to `blastn`, `blastp`, `blastx`, and `makeblastdb`.
The BLAST software needs to be downloaded and installed separately.
Other R interfaces for bioinformatics are also available:
- [rRDP](https://bioconductor.org/packages/rRDP): Interface to the RDP
Classifier
- [rMSA](https://mhahsler.r-universe.dev/rMSA): Interface for Popular
Multiple Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE,
and Kalign
## Installation
1. Install the BLAST software by following the instructions in the
[INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL)
file.
2. Install the latest version of the R package
``` r
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
# The following initializes usage of Bioc devel
BiocManager::install(version = "devel")
BiocManager::install("rBLAST")
```
## Usage
``` r
library(rBLAST)
```
Download the prebuilt 16S Microbial data base from NCBI’s ftp server at:
<https://ftp.ncbi.nlm.nih.gov/blast/db/>
``` r
tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
untar(tgz_file, exdir = "16S_rRNA_DB")
```
Load the downloaded BLAST database.
``` r
bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
bl
```
## BLAST Database
## Location: /home/hahsler/baR/rBLAST/16S_rRNA_DB/16S_ribosomal_RNA
## BLAST Type: blastn
## Database: 16S ribosomal RNA (Bacteria and Archaea type strains)
## 27,138 sequences; 39,323,968 total bases
##
## Date: Apr 9, 2024 5:36 AM Longest sequence: 3,600 bases
##
## BLASTDB Version: 5
##
## Volumes:
## /home/hahsler/baR/rBLAST/16S_rRNA_DB/16S_ribosomal_RNA
Load some test sequences shipped with the package.
``` r
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta", package = "rBLAST"))
seq
```
## RNAStringSet object of length 5:
## width seq names
## [1] 1481 AGAGUUUGAUCCUGGCUCAGAAC...GGUGAAGUCGUAACAAGGUAACC 1675 AB015560.1 d...
## [2] 1404 GCUGGCGGCAGGCCUAACACAUG...CACGGUAAGGUCAGCGACUGGGG 4399 D14432.1 Rho...
## [3] 1426 GGAAUGCUNAACACAUGCAAGUC...AACAAGGUAGCCGUAGGGGAACC 4403 X72908.1 Ros...
## [4] 1362 GCUGGCGGAAUGCUUAACACAUG...UACCUUAGGUGUCUAGGCUAACC 4404 AF173825.1 A...
## [5] 1458 AGAGUUUGAUUAUGGCUCAGAGC...UGAAGUCGUAACAAGGUAACCGU 4411 Y07647.2 Dre...
Query the BLAST database to find matches for the first test sequence
with a 99% percent identity or higher.
``` r
cl <- predict(bl, seq[1, ], BLAST_args = "-perc_identity 99")
cl
```
## qseqid sseqid pident length mismatch gapopen qstart qend sstart send
## 1 1675 NR_151899.1 100 40 0 0 22 61 2 41
## 2 1675 NR_041235.1 100 37 0 0 22 58 2 38
## 3 1675 NR_173526.1 100 35 0 0 32 66 1 35
## 4 1675 NR_117153.1 100 32 0 0 27 58 1 32
## evalue bitscore
## 1 1.5e-12 75
## 2 7.0e-11 69
## 3 9.0e-10 66
## 4 4.2e-08 60
## Citation Request
To cite package ‘rBLAST’ in publications use:
> Hahsler M, Nagar A (2024). “rBLAST: R Interface for the Basic Local
> Alignment Search Tool.” Bioconductor version: Release (3.19).
> <doi:10.18129/B9.bioc.rBLAST>
> <https://doi.org/10.18129/B9.bioc.rBLAST>, R package version 0.99.4.
@Misc{,
title = {{rBLAST:} {R} Interface for the Basic Local Alignment Search Tool},
author = {Michael Hahsler and Annurag Nagar},
year = {2024},
doi = {10.18129/B9.bioc.rBLAST},
note = {R package version 0.99.4},
howpublished = {Bioconductor version: Release (3.19)},
}
## Acknowledgments
This work was partially supported by grant no. R21HG005912 from the
[National Human Genome Research Institute](https://www.genome.gov/).
