README.md

In mhahsler/rBLAST: R Interface for the Basic Local Alignment Search Tool

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

1. Install the Bioconductor package Biostrings following the instructions here.

2. Install rBlast from r-universe using

   r install.packages("rBLAST", repos = "https://mhahsler.r-universe.dev")

3. Install the BLAST software by following the instructions in the INSTALL file.

Usage

library(rBLAST)

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

db <- get_blast_db("16S_ribosomal_RNA")
db

## [1] "/home/hahsler/.cache/R/rBLAST/16S_ribosomal_RNA/16S_ribosomal_RNA"

Load the downloaded BLAST database.

bl <- blast(db = db)
bl

## BLAST Database
## Location: /home/hahsler/.cache/R/rBLAST/16S_ribosomal_RNA/16S_ribosomal_RNA 
## BLAST Type: blastn 
## Database: 16S ribosomal RNA (Bacteria and Archaea type strains)
##  22,242 sequences; 32,333,479 total bases
## 
## Date: Mar 26, 2024  5:36 AM  Longest sequence: 3,600 bases
## 
## BLASTDB Version: 5
## 
## Volumes:
##  /home/hahsler/.cache/R/rBLAST/16S_ribosomal_RNA/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 1.2e-12       75
## 2 5.8e-11       69
## 3 7.4e-10       66
## 4 3.5e-08       60

Citation Request

Cite the use of this package as:

Hahsler M, Nagar A (2019). rBLAST: R Interface for the Basic Local Alignment Search Tool. R package version 0.99.2, URL: https://github.com/mhahsler/rBLAST.

BibTeX

@Manual{,
    title = {{rBLAST: R Interface for the Basic Local Alignment Search Tool}},
    author = {Michael Hahsler and Anurag Nagar},
    year = {2019},
    note = {R package version 0.99.2},
    url = {https://github.com/mhahsler/rBLAST}
  }

mhahsler/rBLAST documentation built on April 14, 2024, 10:22 a.m.