This is an extension of Archarlie's Shiny App that creates SNP-sensitive primers and probes (no probes as of July 2024). This versions attempts to condense it into a package.
- Main files are ria_fxns_draft and the app
- Talk to Bro. Terribilini throughout your development of the code and app
- Next steps are optimizing the app/code and creating a package
- My multiplex testing primers were held on to by Bro. Terribilini so you can test the specificity of the snp-specific primer design from the code
- You will need to find a better temp calculation method (check accuracy of your method with Oligo Analyzer).
- Good luck on your work! If you have any questions for me, my email is rianoble@umich.edu :)
Copy and paste the code below: (Work in Progress)
install.packages("devtools") library(devtools) install_github("rianoble/acornfinder") library(acornfinder)
snpmart <- useMart("ENSEMBL_MART_SNP", dataset = "hsapiens_snp")
Parameters: primer, shift, desired_tm, diff, Heterodimer_tm, Homodimer, top, hairpin
Result: primers
Example:
primer = "rs53576, rs1815739, rs7412, rs429358, rs6152"
primer = "rs9462492, rs58318008, rs1421085" primer = "rs1550576, rs17025867" primer = "rs9462492, rs58318008" primer = "rs1421085, rs9462492" shift = 100 desired_tm = 64 diff = 3 Heterodimer_tm = 50 Homodimer <- 45 top <- 2 hairpin <- 45 output <- findacorn(primer, shift, desired_tm, diff, Heterodimer_tm, Homodimer, top, hairpin)
Attempts to answer all questions in one function. Produces a pop-out output.
-reverse primer has same melting temperature as forward primer -melting temps should be under 1-2 degrees difference -paste in entire sequence retrieved by biomart in r into primer blast (~1000 bases of seq, 500 before, 500 after)
Parameters: primer, shift
Result: generates primers
Example:
Future:
- create a help file? install.packages("roxygen2") library(roxygen2)