Translation tables

By default, Codeine uses the standard genetic code. It can also be used to generate sequences under nonstandard genetic codes.

Choosing a translation table

The TranslationTable object governs how Codeine translates and reverse-translates amino acid sequences. A table can be chosen from the NCBI list of genetic code tables by specifying its ID:

from codeine import TranslationTable

table1 = TranslationTable(table_id=1)

print(table1.name)
print('M', table1.aa_to_codons['M'])

table2 = TranslationTable(table_id=2)

print(table2.name)
print('M', table2.aa_to_codons['M'])

Output:

Standard
M ('ATG',)
Vertebrate Mitochondrial
M ('ATA', 'ATG')

To use a nonstandard genetic code with Codeine, simply pass one to the CodingSpace:

from codeine import CodingSpace, TranslationTable

table = TranslationTable(table_id=2)

space = CodingSpace('CYIQNCPLG', translation_table=table)

Custom tables

Codeine also supports user-defined custom tables:

from codeine import TranslationTable

table = TranslationTable.custom(
    codons_to_aa={
        'AAA': 'A',
        'AAC': 'B',
        'AAG': 'C',
        'AAT': 'D',
        'ACA': 'E',
        'ACC': 'F',
        'ACG': 'G',
        'ACT': '*',
    },
)

print(table.codons_to_aa['AAG'])

RNA tables

By default, translation tables use DNA codons. To use RNA codons instead, set rna=True.

table = TranslationTable(table_id=1, rna=True)

print(table.translate['M'])

Available tables

Codeine supports the following NCBI genetic code tables:

ID	Name
1	Standard
2	Vertebrate Mitochondrial
3	Yeast Mitochondrial
4	Mold Mitochondrial
5	Invertebrate Mitochondrial
6	Ciliate Nuclear
9	Echinoderm Mitochondrial
10	Euplotid Nuclear
11	Bacterial
12	Alternative Yeast Nuclear
13	Ascidian Mitochondrial
14	Alternative Flatworm Mitochondrial
15	Blepharisma Macronuclear
16	Chlorophycean Mitochondrial
21	Trematode Mitochondrial
22	Scenedesmus obliquus Mitochondrial
23	Thraustochytrium Mitochondrial
24	Pterobranchia Mitochondrial
25	Candidate Division SR1
26	Pachysolen tannophilus Nuclear
27	Karyorelict Nuclear
28	Condylostoma Nuclear
29	Mesodinium Nuclear
30	Peritrich Nuclear
31	Blastocrithidia Nuclear
32	Balanophoraceae Plastid
33	Cephalodiscidae Mitochondrial

Fixed codons

codon_restrictions restricts which codons are allowed at specific amino acid positions. They can either be fixed exact codons, or subsets of the set of possible codons for that amino acid. Positions are 1-based.

from codeine import CodingSpace

aa_seq = 'MKTLEFQNGSCPRYKKL'

space = CodingSpace(
   aa_seq,
   codon_restrictions={
       2: 'AAA',
       3: ['ACA', 'ACG'],
   },
   seed=42,
)

Here, position 1 is restricted to TCG or TCA, and position 2 is fixed to GAG.