Codeine

Codeine is a Python library for exploring synonymous coding sequence spaces under biological constraints.

Why Codeine?

Codeine compiles biological constraints into a CodingSpace, an exact representation of the feasible design space for a given amino acid sequence.

Sequences sampled or enumerated from a CodingSpace are automatically valid under the specified constraints. This means sequences can be generated freely and scored according to arbitrary objective functions, without sequence repair or filtering.

Features

• Arbitrarily long amino acid sequences

• Exact counting of sequence spaces

• Sequence enumeration

• Uniform and weighted sampling

• Local sequence redesign

• Mutation spaces

• Fixed codons

• Sequence contexts

• Restriction sites & arbitrary motif avoidance

• Homopolymer and tandem repeat avoidance

• Custom translation tables

Example

from codeine import CodingSpace, RestrictionSite

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

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