dense-arrays

dense-arrays is a library for designing double-stranded nucleotide sequences with densely packed DNA-protein binding sites, which we name the nucleotide String Packing Problem (SPP), related to the classical Shortest Common Superstring problem in theoretical computer science.

For more detailed documentation, please visit our documentation site.

Formulation of the nucleotide String Packing Problem (SPP) as an Orienteering Problem (OP). For more details, see the associated paper.

Installation

1. (Optional but Recommended) Create a Conda Environment
   Create and activate a new environment:

   conda create -n dense-arrays python
   conda activate dense-arrays

2. Install the Package
   Use pip to install:

   pip install .

Simple Usage

Here's an example that demonstrates how to use dense-arrays:

import dense_arrays as da

# Define a list of nucleotide motifs and initialize the optimizer with a target sequence length.
opt = da.Optimizer([
    "ATAATATTCTGAATT",
    "TCCCTATAAGAAAATTA",
    "TAATTGATTGATT",
    "GCTTAAAAAATGAAC",
    "TGCACTAAAATGGTGCAA",
], sequence_length=30)

# Find and print the optimal solution.
best = opt.optimal()
print(f"Optimal solution, score {best.nb_motifs}")
print(best)

# List and print all possible solutions.
print("List of all solutions")
for solution in opt.solutions():
    print(f"Solution with score {solution.nb_motifs}:")
    print(solution)

Solver Backends

The methods Optimizer.optimal and Optimizer.solutions allow you to specify a solver backend. They accept any solver supported by ortools. The available options include:

• "CBC" (default)
• "SCIP"
• "GUROBI"
• "CPLEX"
• "XPRESS"
• "GLPK"