Codeine

Codeine is a Python library for constrained reverse translation of protein sequences.

Example

from codeine import CodingSpace, RestrictionSite
from codeine.constraints import ForbiddenMotifs, MaxHomopolymer

space = CodingSpace(
    'CYIQNCPLG',
    constraints=[
        ForbiddenMotifs(RestrictionSite.EcoRI),
        MaxHomopolymer(5),
    ],
)

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

Why Codeine?

Codeine compiles biological constraints into a CodingSpace, an exact representation of the feasible coding sequence 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