celalp / rblast

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

rBLAST - Interface for BLAST search (R-Package)

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.

Installation

1. Install the package devtools.
2. Install the Bioconductor package Biostrings either using devtools::install_bioc("Biostrings") or directly from Bioconductor.
3. Install rBlast from GitHub using devtools::install_github("mhahsler/rBLAST").
4. Install the BLAST software by following the instructions found in ? 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 data 
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