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
-
Install the Bioconductor package
Biostringsfollowing the instructions here. -
Install the
rBlastfrom r-universe usinginstall.packages('rBLAST', repos = 'https://mhahsler.r-universe.dev')
-
Install the BLAST software by following the instructions found in
library('rBLAST') ? blast
library(rBLAST)Download the 16S Microbial data base from NCBI
download.file("https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz",
"16S_ribosomal_RNA.tar.gz", mode='wb')
untar("16S_ribosomal_RNA.tar.gz", exdir="16SMicrobialDB")Load some test sequences
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...
Load a BLAST database (replace db with the location + name of the BLAST DB)
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)
## 21,856 sequences; 31,790,086 total bases
##
## Date: May 1, 2021 5:36 AM Longest sequence: 3,600 bases
##
## BLASTDB Version: 5
##
## Volumes:
## /home/hahsler/baR/rBLAST/16S_rRNA_DB/16S_ribosomal_RNA
Query a sequence using BLAST and find sequences with a 99% percent identity or higher.
cl <- predict(bl, seq[1,], BLAST_args = "-perc_identity 99")
cl## QueryID SubjectID Perc.Ident Alignment.Length Mismatches Gap.Openings
## 1 1675 NR_151899.1 100 40 0 0
## 2 1675 NR_041235.1 100 37 0 0
## 3 1675 NR_036779.1 100 34 0 0
## 4 1675 NR_117153.1 100 32 0 0
## Q.start Q.end S.start S.end E Bits
## 1 22 61 2 41 1.22e-12 75.0
## 2 22 58 2 38 5.66e-11 69.4
## 3 24 57 2 35 2.63e-09 63.9
## 4 27 58 1 32 3.40e-08 60.2
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}
}
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