An R package to ease primer design using Primer3.
You can install primex from github with:
# install.packages("devtools") devtools::install_github("dieterich-lab/primex")
library(primex) exonSeqs <- c( exon1 = paste0( "CTCACCATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGGCATGTGCAAG", "GCCGGCTTCGCGGGCGACGATGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGC", "AGGCACCAG" ), exon2 = paste0( "GGCGTGATGGTGGGCATGGGTCAGAAGGATTCCTATGTGGGCGACGAGGCCCAGAGCAAG", "AGAGGCATCCTCACCCTGAAGTACCCCATCGAGCACGGCATCGTCACCAACTGGGACGAC", "ATGGAGAAAATCTGGCACCACACCTTCTACAATGAGCTGCGTGTGGCTCCCGAGGAGCAC", "CCCGTGCTGCTGACCGAGGCCCCCCTGAACCCCAAGGCCAACCGCGAGAAGATGACCCAG" ) ) seqOpts <- seqSettings(seqId = "transcript2", seq = exonSeqs) p3Opts <- p3Settings() %>% primerTm(min = 58, optimal = 63, max = 67) primers <- design(seqOpts, p3Opts)
First two candidate pairs:
| first | second | |
|---|---|---|
| PRIMER_PAIR_PENALTY | 4.488355 | 4.494866 |
| PRIMER_LEFT_PENALTY | 4.462257 | 0.032609 |
| PRIMER_RIGHT_PENALTY | 0.026098 | 4.462257 |
| PRIMER_LEFT_SEQUENCE | ACCAGGGCGTGATGGTGG | ATGGATGATGATATCGCCGC |
| PRIMER_RIGHT_SEQUENCE | CATGTCGTCCCAGTTGGTGA | CCACCATCACGCCCTGGT |
| PRIMER_LEFT | 117,18 | 6,20 |
| PRIMER_RIGHT | 244,20 | 134,18 |
| PRIMER_LEFT_TM | 65.462 | 63.033 |
| PRIMER_RIGHT_TM | 63.026 | 65.462 |
| PRIMER_LEFT_GC_PERCENT | 66.667 | 50.000 |
| PRIMER_RIGHT_GC_PERCENT | 55.000 | 66.667 |
| PRIMER_LEFT_SELF_ANY_TH | 6.11 | 0.00 |
| PRIMER_RIGHT_SELF_ANY_TH | 0.00 | 0.00 |
| PRIMER_LEFT_SELF_END_TH | 0.00 | 0.00 |
| PRIMER_RIGHT_SELF_END_TH | 0.00 | 0.00 |
| PRIMER_LEFT_HAIRPIN_TH | 43.01 | 27.69 |
| PRIMER_RIGHT_HAIRPIN_TH | 32.56 | 43.06 |
| PRIMER_LEFT_END_STABILITY | 9.4000 | 12.9000 |
| PRIMER_RIGHT_END_STABILITY | 7.9000 | 7.9000 |
| PRIMER_PAIR_COMPL_ANY_TH | 0.00 | 0.62 |
| PRIMER_PAIR_COMPL_END_TH | 5.31 | 0.00 |
| PRIMER_PAIR_PRODUCT_SIZE | 128 | 129 |