cutfree: Design degenerate oligos free of restriction sites

In pauljensen/cutfree: Design DNA Barcodes without Restriction Sites

Description

Design pools of DNA oligos that are guaranteed to not contain specified restriction enzyme cut sites. All cut sites are blocked while ensuring the optimal number of oligos remain in the pool.

Usage

cutfree(len = 20, sites = c(), codes = IUB_CODES,
  starting_oligo = strrep("N", len), min_blocks = 1,
  obj_weights = log(1:4), re_randomize = TRUE, seed = NULL,
  obj_frac = 1, quiet = FALSE, maxtime = 30)

Arguments

len	Length of the random oligo. Must be provided if starting_oligo is not given.
sites	Character vector of restriction sites to block.
starting_oligo	Starting oligo from which sites will be removed. If not given, defaults to a string of N's.
min_blocks	Minimum number of blocks at each site, i.e. the minimum number of changes that need to be made for a cut site to appear anywhere in the oligo.
obj_weights	Objective function weights for each code's degeneracy.
re_randomize	If TRUE (default), re-run the optimization to randomize the codes while maintaining the same number of oligos.
seed	Seed for the random number generator.
obj_frac	Fraction of the objective function that must be maintained during re-randomization.
quiet	Run silently with no output from Gurobi.
maxtime	Maximum time (in seconds) allowed for the solver.

Value

A list containing code – the randomize oligo, and a fields describing the MILP and the solution statistics.

Examples

result <- cutfree(m=20, sites=c("GGTCTC", "GATATC"), min_blocks=2)
print_degenerate_oligo(result$code)

pauljensen/cutfree documentation built on March 26, 2020, 12:45 p.m.