primer.insilico: Find primer pairs in BLAST results

Description Usage Arguments Value Examples

Description

Find primer pairs in BLAST results

Usage

1
2
primer.insilico(x, filt = (pident >= 80 & length/slen >= 0.8),
  size.range = c(50, 1200))

Arguments

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.

Value

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

Examples

 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)

zachth/RinsilicoPCR documentation built on May 29, 2019, 12:19 p.m.