R package for easier primer design from multiple sequence alignments
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README.md

prider - easy primer design from multiple sequence alignments in R

Description

prider is an R tool that facilitates probe and primer design for multiple sequence alignments by locating highly conserved regions.

Usage

Takes a fasta input as ape sequence object. Produces a list of primer candidates.

Requirements

Tested on R 3.2.0

Installation

Install the development version from github:

# install.packages("devtools")
devtools::install_github("manutamminen/prider")

Examples

data(test_dna_alignment)

#Plot the conservation score
make_consensus(test_dna_alignment) %>% ggplot(aes(x=L1, y=value)) + geom_point()

#Find the primer candidates
find_primers(test_dna_alignment, 0.7, length=20, cutoff=2)