Description Usage Arguments Value Examples
Find primer pairs in BLAST results
1 2 | primer.insilico(x, filt = (pident >= 80 & length/slen >= 0.8),
size.range = c(50, 1200))
|
x |
data.frame of BLAST results |
filt |
Logical expression used to filter mismatches from primer BLAST results. Defaults to 'pident >= 80 & length/slen >= .8', (percent identity > 80% and match length > 80% of primer). |
size.range |
numeric vector of length 2 giving the range of expected amplicon length. |
list of results for each query sequence containing:
dir : orientation of amplicon
blastres : BLAST table results for primer pair
location : start and end coordinates for the amplicon
size : size of the amplicon
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ##Run local primer blast
query <- readDNAStringSet("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/010/525/GCA_000010525.1_ASM1052v1/GCA_000010525.1_ASM1052v1_genomic.fna.gz")
primers <- c("GGCTGGATCACCTCCTT","GCCWAGGCATCCDCC")
db <- makeprimerdb(primers)
#Define BLAST arguments: these are the same that can be found in `RinsilicoPCR::blast.params$primers`
args <- list(
outfmt="'6 qacc sacc pident length qlen slen qstart sstart qend send evalue'",
max_target_seqs=20,
word_size=8
)
blastres <- blast(query,db,args)
pairs <- primer.insilico(blastres)
|
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