View source: R/blast_protein_to_nr_database.R
blast_protein_to_nr_database | R Documentation |
Run protein to protein BLAST of reference sequences against the NCBI non-redundant protein sequence Database.
blast_protein_to_nr_database(
query,
nr.database,
nr.needs.formatting = FALSE,
output.path = NULL,
task = "blastp",
db.import = FALSE,
postgres.user = NULL,
evalue = 1e-05,
out.format = "csv",
cores = 1,
max.target.seqs = 65200,
db.soft.mask = TRUE,
db.hard.mask = TRUE,
blast.path = NULL
)
query |
path to input file in fasta format. |
nr.database |
path to local NCBI NR database. |
nr.needs.formatting |
a logical value indicating whether or not the local database specified in |
output.path |
path to folder at which BLAST output table shall be stored.
Default is |
task |
protein search task option. Options are:
|
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 BLAST results shall be stored. Available options are:
|
cores |
number of cores for parallel BLAST searches. |
max.target.seqs |
maximum number of aligned sequences that shall be retained. Please be aware that |
db.soft.mask |
shall low complexity regions be soft masked? Default is |
db.hard.mask |
shall low complexity regions be hard masked? Default is |
blast.path |
path to BLAST executables. |
Hajk-Georg Drost
blast_nucleotide_to_nucleotide
, blast_nucleotide_to_protein
,
blast_protein_to_nucleotide
, blast_best_hit
## Not run:
blast_example <- blast_protein_to_nr_database(
query = system.file('seqs/qry_aa.fa', package = 'metablastr'),
nr.database = "nr",
output.path = tempdir(),
db.import = FALSE)
# look at BLAST results
blast_example
## End(Not run)
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