make_blast_DB | R Documentation |
Builds a BLAST database with local sequences using FASTA file.
make_blast_DB( makeblastdb.way, fasta.way, db.way, db.type = "nucl", db.title, delete.fasta = FALSE, verbose = TRUE )
makeblastdb.way |
character; name and path to makeblastdb executable file |
fasta.way |
character; name and path to FASTA file |
db.way |
character; name and path to local BLAST database |
db.type |
character; type of BLAST database |
db.title |
character; BLAST data base title |
delete.fasta |
logical; delete FASTA file |
verbose |
logical; show messages |
This function is using BLAST applications. BLAST+ (UNIX or Windows) should be installed.
The function creates local BLAST data base. No additional data is returned.
Elena N. Filatova
Camacho C., Coulouris G., Avagyan V. et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10, 421. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-421.
## Not run: # This function is using BLAST applications. BLAST+ should be installed. # FASTA file with sequences for local data base should be downloaded first (see get_seq_for_DB ()) path <- tempdir() dir.create (path) # load metadata for target sequences of Chlamydia pneumoniae (meta.target) # load sequences, it will take about 3 minutes get_seq_for_DB (ids = meta.target$gi, db = "nucleotide", check.result = TRUE, return="fasta", fasta.file = paste0 (path, "/seq.fasta"), verbose = TRUE) # create local data base, it will take 0.235217 seconds make_blast_DB (makeblastdb.way = "D:/Blast/blast-2.11.0+/bin/makeblastdb.exe", fasta.way = paste0 (path, "/seq.fasta"), db.title = "Cl_pneumoniae", db.way = paste0 (path, "/DB"), db.type = "nucl", delete.fasta = FALSE) # delete FASTA file (also can set delete.fasta = TRUE) file.remove (paste0 (path, "/seq.fasta")) ## End(Not run)
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