GitHub - mhahsler/rBLAST: Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package (original) (raw)

R package rBLAST - R Interface for the Basic Local Alignment Search Tool

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: Interface to the RDP Classifier
rMSA: Interface for Popular Multiple Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign

Installation

Install the BLAST software by following the instructions in theINSTALLfile.
Install the latest version of the R package
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}

The following initializes usage of Bioc devel

BiocManager::install(version = "devel")
BiocManager::install("rBLAST")

Usage

Download the prebuilt 16S Microbial data base from NCBI’s ftp server at:https://ftp.ncbi.nlm.nih.gov/blast/db/

tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz") untar(tgz_file, exdir = "16S_rRNA_DB")

Load the downloaded BLAST database.

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.

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.

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.rBLASThttps://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 theNational Human Genome Research Institute.