/rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

Primary LanguageRGNU General Public License v3.0GPL-3.0

rBLAST - R Interface for the Basic Local Alignment Search Tool (BLAST)

rBLAST r-universe status

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 the rBlast from r-universe using 
    install.packages('rBLAST', repos = 'https://mhahsler.r-universe.dev')
  3. Install the BLAST software by following the instructions found in 
    library('rBLAST')
? blast

Usage

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')
trying URL 'https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz'
Content type 'application/x-gzip' length 37346728 bytes (35.6 MB)
==================================================
downloaded 35.6 MB

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 AGAGUUUGAUCCUGGCUCAGAACGAACGCUGG...GGUGAUCGGGGUGAAGUCGUAACAAGGUAACC 1675
[2]  1404 GCUGGCGGCAGGCCUAACACAUGCAAGUCGAA...GCAGCCGACCACGGUAAGGUCAGCGACUGGGG 4399
[3]  1426 GGAAUGCUNAACACAUGCAAGUCGCACGGGCA...UGUAGUCGNAACAAGGUAGCCGUAGGGGAACC 4403
[4]  1362 GCUGGCGGAAUGCUUAACACAUGCAAGUCGCA...AGUUGGUUUUACCUUAGGUGUCUAGGCUAACC 4404
[5]  1458 AGAGUUUGAUUAUGGCUCAGAGCGAACGCUGG...CGACUGGGGUGAAGUCGUAACAAGGUAACCGU 4411

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

cl <- predict(bl, seq[1,])
cl[1:5,]
  QueryID   SubjectID Perc.Ident Alignment.Length Mismatches Gap.Openings Q.start Q.end S.start
1    1675 NR_104821.1     90.816             1459        124            8      16  1468       5
2    1675 NR_117601.1     85.896             1255        160           15     229  1478     237
3    1675 NR_117601.1     93.846               65          4            0       5    69       1
4    1675 NR_074549.1     85.896             1255        160           15     229  1478     241
5    1675 NR_074549.1     94.203               69          4            0       1    69       1
  S.end        E Bits
1  1459 0.00e+00 1943
2  1479 0.00e+00 1321
3    65 7.21e-20   99
4  1483 0.00e+00 1321
5    69 4.31e-22  106

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},
  }