search_primer_pair {primerTree} | R Documentation |
Automatic primer searching Search a given primer pair, retrieving the alignment results, their product sequences, the taxonomic information for the sequences, a multiple alignment of the products
Description
Automatic primer searching Search a given primer pair, retrieving the alignment results, their product sequences, the taxonomic information for the sequences, a multiple alignment of the products
Usage
search_primer_pair(
forward,
reverse,
name = NULL,
num_aligns = 500,
num_permutations = 25,
simplify = TRUE,
clustal_options = list(),
distance_options = list(model = "N", pairwise.deletion = T),
api_key = Sys.getenv("NCBI_API_KEY"),
...,
.parallel = FALSE,
.progress = "none"
)
Arguments
forward |
forward primer to search by 5'-3' on plus strand |
reverse |
reverse primer to search by 5'-3' on minus strand |
name |
name to give to the primer pair |
num_aligns |
number of alignment results to keep |
num_permutations |
the number of primer permutations to search, if the degenerate bases cause more than this number of permutations to exist, this number will be sampled from all possible permutations. |
simplify |
use simple names for primer hit results or complex |
clustal_options |
a list of options to pass to clustal omega, see
|
distance_options |
a list of options to pass to dist.dna, see
|
api_key |
NCBI api-key to allow faster sequence retrieval |
... |
additional arguments passed to Primer-Blast |
.parallel |
if 'TRUE', perform in parallel, using parallel backend provided by foreach |
.progress |
name of the progress bar to use, see
|
Value
A list with the following elements,
name |
name of the primer pair |
BLAST_result |
html blast results from Primer-BLAST as
'a |
object.
taxonomy |
taxonomy for the primer products from NCBI |
sequence |
sequence of the primer products |
alignment |
multiple alignment of the primer products |
tree |
phylogenetic tree of the reconstructed from the 'multiple alignment |
See Also
Examples
## Not run:
#simple search
mammals_16S = search_primer_pair(name='Mammals 16S',
'CGGTTGGGGTGACCTCGGA', 'GCTGTTATCCCTAGGGTAACT')
#returning 1000 alignments, allow up to 3 mismatches in primer
mammals_16S = search_primer_pair(name='Mammals 16S',
'CGGTTGGGGTGACCTCGGA', 'GCTGTTATCCCTAGGGTAACT',
num_aligns=1000, total_primer_specificity_mismatch=3)
## End(Not run)