View source: R/blast_best_reciprocal_hit.R
blast_best_reciprocal_hit | R Documentation |
This function performs a BLAST search between query and subject sequences reciprocally and returns (for each direction) only the best hit based on the following criteria.
A best blast hit is defined as:
the hit with the smallest e-value
if e-values are identical then the hit with the longest alignment length is chosen
A best reciprocal BLAST hit is defined as a hit that fulfills the following symmetry criteria:
blast_best_hit(A,B) = blast_best_hit(B,A)
blast_best_reciprocal_hit(
query,
subject,
search_type = "nucleotide_to_nucleotide",
strand = "both",
output.path = NULL,
is.subject.db = FALSE,
task = "blastn",
db.import = FALSE,
postgres.user = NULL,
evalue = 0.001,
out.format = "csv",
cores = 1,
max.target.seqs = 10000,
db.soft.mask = FALSE,
db.hard.mask = FALSE,
blast.path = NULL
)
query |
path to input file in fasta format. |
subject |
path to subject file in fasta format or blast-able database. |
search_type |
type of query and subject sequences that will be compared via BLAST search. Options are:
|
strand |
Query DNA strand(s) to search against database/subject. Options are:
|
output.path |
path to folder at which BLAST output table shall be stored.
Default is |
is.subject.db |
logical specifying whether or not the |
task |
BLAST search task option (depending on the selected
|
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_protein_to_protein
,
blast_nucleotide_to_protein
, blast_protein_to_nucleotide
, blast_best_hit
## Not run:
test_best_reciprocal_hit <- blast_best_reciprocal_hit(
query = system.file('seqs/qry_nn.fa', package = 'metablastr'),
subject = system.file('seqs/sbj_nn_best_hit.fa', package = 'metablastr'),
search_type = "nucleotide_to_nucleotide",
output.path = tempdir(),
db.import = FALSE)
# look at results
test_best_reciprocal_hit
## End(Not run)
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