synbiopython.codon.utils

Synbiopython (c) Global BioFoundry Alliance 2020

Synbiopython is licensed under the MIT License.

To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.

@author: neilswainston

synbiopython.codon.utils.optimise(table, aa_seq)[source]

Codon optimise an amino acid sequence.

Parameters
  • table (str) – a codon usage table.

  • aa_seq – an amino acid sequence.

Returns

a codon-optimised nucleic acid sequence, encoding the supplied amino acid sequence

Return type

str

synbiopython.codon.utils.sample(table, amino_acid)[source]

Sample a codon for a given amino acid probabilistically, based on its codon usage frequency.

Parameters
  • table (dict) – a codon usage table.

  • amino_acid (str) – a single-character string representing an amino acid.

Returns

a codon encoding the supplied amino acid, sampled probabilistically.

Return type

str