Codeine

Codeine is a Python library for exploring constrained synonymous coding sequence spaces.

Overview

Codeine represents the complete space of synonymous coding sequences satisfying user-defined constraints. This makes it possible to count, sample and enumerate valid coding sequences exactly.

Traditional codon optimisation tools typically return a single sequence. By contrast, Codeine represents the full feasible sequence space, allowing users to explore alternative designs freely.

Constraints are built in to Codeine’s sequence generation process, so that all generated sequences are automatically valid. This means you can generate as many sequences as needed and score them according to your own objective functions, without having to repair or filter them.

Features

• Exact counting of sequence spaces

• Uniform and weighted sampling

• Sequence enumeration

• Local sequence redesign

• Mutation spaces

• Restriction site avoidance

• Homopolymer constraints

• Custom translation tables

Example

from codeine import CodingSpace, RestrictionSite

space = CodingSpace(
    'SEQVENCE',
    forbidden_motifs=[RestrictionSite.EcoRI],
    max_homopolymer=5
)

print(space.n_valid_sequences)
print(space.sample())