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

• Install Bioconductor and the Bioconductor package Biostrings.
• Download and install the package from AppVeyor or install via install_github("mhahsler/rBLAST") (requires the R package devtools)
• Install the BLAST software by following the instructions found in ? blast

Usage

## download the 16S Microbial data base from NCBI
download.file("ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz",
    "16SMicrobial.tar.gz", mode='wb')

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz'
ftp data connection made, file length 4192539 bytes
==================================================
downloaded 4.0 MB

untar("16SMicrobial.tar.gz", exdir="16SMicrobialDB")

## load some test data 
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
                        package="rBLAST"))
seq

  A RNAStringSet instance of length 5
    width seq                                                                    names               
[1]  1481 AGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCG...UGGUGAUCGGGGUGAAGUCGUAACAAGGUAACC 1675
[2]  1404 GCUGGCGGCAGGCCUAACACAUGCAAGUCGAACG...GGCAGCCGACCACGGUAAGGUCAGCGACUGGGG 4399
[3]  1426 GGAAUGCUNAACACAUGCAAGUCGCACGGGCAGC...GUGUAGUCGNAACAAGGUAGCCGUAGGGGAACC 4403
[4]  1362 GCUGGCGGAAUGCUUAACACAUGCAAGUCGCACG...GAGUUGGUUUUACCUUAGGUGUCUAGGCUAACC 4404
[5]  1458 AGAGUUUGAUUAUGGCUCAGAGCGAACGCUGGCG...GCGACUGGGGUGAAGUCGUAACAAGGUAACCGU 4411

## load a BLAST database (replace db with the location + name of the BLAST DB)
bl <- blast(db="./16SMicrobialDB/16SMicrobial")
bl

BLAST Database
Location: /home/hahsler/baR/rMSA/16SMicrobialDB/16SMicrobial 
Database: 16S Microbial Sequences
	17,624 sequences; 25,680,771 total bases

Date: Jun 2, 2015  12:00 AM	Longest sequence: 2,211 bases

Volumes:
	/home/hahsler/baR/rMSA/16SMicrobialDB/16SMicrobial

## query a sequence using BLAST
cl <- predict(bl, seq[1,])
cl[1:5,]

  QueryID                     SubjectID Perc.Ident Alignment.Length Mismatches Gap.Openings Q.start
1    1675 gi|559795231|ref|NR_104821.1|      90.82             1459        124            8      16
2    1675 gi|444304125|ref|NR_074549.1|      85.99             1249        158           15     235
3    1675 gi|444304125|ref|NR_074549.1|      94.20               69          4            0       1
4    1675 gi|645320383|ref|NR_117601.1|      85.99             1249        158           15     235
5    1675 gi|645320383|ref|NR_117601.1|      93.85               65          4            0       5
  Q.end S.start S.end     E Bits
1  1468       5  1459 0e+00 1943
2  1478     247  1483 0e+00 1321
3    69       1    69 3e-22  106
4  1478     243  1479 0e+00 1321
5    69       1    65 6e-20   99