View source: R/blast_rpsblast.R
blast_rpsblast | R Documentation |
Run rpsblast (Reverse PSI-BLAST) searches a query sequence against a database of profiles, or score matrices, producing BLAST-like output.
blast_rpsblast(
query,
db,
db.alias,
prep.db = FALSE,
output.path = NULL,
db.import = FALSE,
postgres.user = NULL,
evalue = 0.001,
out.format = "csv",
cores = 1,
blast.path = NULL
)
query |
path to input file in fasta format. |
db |
path to rpsblast-able database or smp files if |
db.alias |
alias for database files |
prep.db |
logical, default FALSE; if TRUE - prep db before running rpsblast. |
output.path |
path to folder at which BLAST output table shall be stored. |
db.import |
shall the BLAST output be stored in a PostgresSQL database and shall a connection be established to this database? Default is |
postgres.user |
when |
evalue |
Expectation value (E) threshold for saving hits (default: |
out.format |
a character string specifying the format of the file in which the rpsblast results shall be stored. Available options are:
|
cores |
number of cores for parallel rpsblast searches. |
blast.path |
path to rpsblast executables. |
Hajk-Georg Drost, Anna Gogleva
blast_protein_to_protein
, blast_nucleotide_to_protein
## Not run:
db_path <- '/home/Cdd'
db_alias <- 'myCdd'
rps_test <- blast_rpsblast(query = system.file('seqs/sbj_aa.fa', package = 'metablastr'),
db = db_path,
db.alias = db_alias,
prep.db = FALSE)
## End(Not run)
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