biopython v1.71.0 Bio.Data.CodonTable

Codon tables based on those from the NCBI.

These tables are based on parsing the NCBI file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt using Scripts/update_ncbi_codon_table.py

Last updated at Version 4.0

Link to this section Summary

Extends a codon list to include all possible ambigous codons

Back a back-table (naive single codon mapping)

Turns codon table data into objects, and stores them in the dictionaries (PRIVATE)

list_ambiguous_codons()

Extends a codon list to include all possible ambigous codons.

e.g.::

 ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR']
 ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA']

Note that [‘TAG’, ‘TGA’] -> [‘TAG’, ‘TGA’], this does not add ‘TRR’. Thus only two more codons are added in the following:

e.g.::

['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

Returns a new (longer) list of codon strings.

make_back_table()

Back a back-table (naive single codon mapping).

ONLY RETURNS A SINGLE CODON, chosen from the possible alternatives based on their sort order.

register_ncbi_table()

Turns codon table data into objects, and stores them in the dictionaries (PRIVATE).