Use EMBOSS primersearch for in silico PCR
A pair of primers are aligned against a set of sequences. The location of the best hits, quality of match, and predicted amplicons are returned. Requires the EMBOSS tool kit (http://emboss.sourceforge.net/) to be installed.
primersearch(input, forward, reverse, mismatch = 5, ...)"primersearch"(input, forward, reverse, mismatch = 5, ...)"primersearch"(input, forward, reverse, mismatch = 5, sequence_col = "sequence", result_cols = NULL, ...)
characterof length 1) The forward primer sequence
characterof length 1) The reverse primer sequence
- An integer vector of length 1. The percentage of mismatches allowed.
characterof length 1) The name of the column in
obs_datathat has the input sequences.
character) The names of columns to include in the output. By defualt, all output columns are included.
An object of type
The command-line tool "primersearch" from the EMBOSS tool kit is needed to use this function.
How you install EMBOSS will depend on your operating system: Linux: Open up a terminal and type:
sudo apt-get install emboss Mac OSX: The easiest way to install EMBOSS on OSX is to use homebrew.
After installing homebrew, open up a terminal and type:
brew install homebrew/science/emboss NOTE: This has not been tested by us yet. Windows: There is an installer for Windows here: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-220.127.116.11-setup.exe NOTE: This has not been tested by us yet.
## Not run: # result <- primersearch(rdp_ex_data, # forward = c("U519F" = "CAGYMGCCRCGGKAAHACC"), # reverse = c("Arch806R" = "GGACTACNSGGGTMTCTAAT"), # mismatch = 10) # # heat_tree(result, # node_size = n_obs, # node_label = name, # node_color = prop_amplified, # node_color_range = c("red", "yellow", "green"), # node_color_trans = "linear", # node_color_interval = c(0, 1), # layout = "fruchterman-reingold") # ## End(Not run)