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.
- Install Bioconductor and the Bioconductor package
Biostrings. - Download and install the package from AppVeyor or install via
install_github("mhahsler/rBLAST")(requires the R packagedevtools) - Install the BLAST software by following the instructions found in
? blast
## download the 16S Microbial data base from NCBI
R> 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
R> untar("16SMicrobial.tar.gz", exdir="16SMicrobialDB")
## load some test data
R> seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
+ package="rBLAST"))
R> 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)
R> bl <- blast(db="./16SMicrobialDB/16SMicrobial")
R> blBLAST 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
R> cl <- predict(bl, seq[1,])
R> 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
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