R code, generate sequences for PCR paper exercises

For bio125 , paper PCR exercises


# Generate sequences for PCR paper exericses

library("seqinr");

list.files()

# Load plasmid pMSH2 sequence into R
seqs = read.fasta( "pMSH2.seq")

# look at the first sequence
seq1 = seqs[[1]]
seq1 = toupper(seq1[1:91])
seq1RC = toupper(rev(comp(seq1)))

c2s(seq1) #sense strand
c2s(seq1RC) #antisense stand

Online primer design tools

http://www.ncbi.nlm.nih.gov/tools/primer-blast/

http://primer3.ut.ee/cgi-bin/primer3/primer3web_results.cgi