callPrimer3

Description

call primer3 for a given set of DNAstringSet object

Usage

1
2
3
4
5
callPrimer3(seq, size_range = "150-500", Tm = c(57, 59, 62),
  name = "Primer1", primer3 = "primer3-2.3.7/bin/primer3_core",
  thermo.param = "primer3-2.3.7/src/primer3_config/",
  sequence_target = NULL,
  settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt")

Arguments

seq

DNAstring object, one DNA string for the given amplicon

size_range

default: '151-500'

Tm

melting temprature parameters default:c(55,57,58)

name

name of the amplicon in chr_start_end format

primer3

primer3 path

thermo.param

thermodynamic parameters folder

sequence_target

If one or more targets is specified then a legal primer pair must flank at least one of them.

settings

text file for parameters

Details

modified to include SEQUENCE_TARGET as an option

Value

data.frame of designed primers and parameters

Author(s)

Altuna Akalin's modified Arnaud Krebs' original function further modified here by Diana Low

Examples

1
2
### NOT RUN ###
# primer_results<-callPrimer3(seq='')