Available genetic codes#

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"
from cogent3 import available_codes

available_codes()
Specify a genetic code using either 'Name' or Code ID (as an integer or string)
Code IDName
1Standard
2Vertebrate Mitochondrial
3Yeast Mitochondrial
4Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
5Invertebrate Mitochondrial
6Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
9Echinoderm Mitochondrial; Flatworm Mitochondrial
10Euplotid Nuclear
11Bacterial, Archaeal and Plant Plastid
12Alternative Yeast Nuclear
13Ascidian Mitochondrial
14Alternative Flatworm Mitochondrial
15Blepharisma Macronuclear
16Chlorophycean Mitochondrial
21Trematode Mitochondrial
22Scenedesmus obliquus Mitochondrial
23Thraustochytrium Mitochondrial
24Rhabdopleuridae Mitochondrial
25Candidate Division SR1 and Gracilibacteria
26Pachysolen tannophilus Nuclear
27Karyorelict Nuclear
28Condylostoma Nuclear
29Mesodinium Nuclear
30Peritrich Nuclear
31Blastocrithidia Nuclear
32Balanophoraceae Plastid
33Cephalodiscidae Mitochondrial

27 rows x 2 columns

Getting a genetic code with get_code()#

This function can be used directly to get a genetic code. We will get the code with ID 4.

from cogent3 import get_code

gc = get_code(4)
gc
Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
aaIUPAC codecodons
AlanineAGCT,GCC,GCG,GCA
CysteineCTGT,TGC
Aspartic AcidDGAT,GAC
Glutamic AcidEGAA,GAG
PhenylalanineFTTC,TTT
GlycineGGGA,GGC,GGT,GGG
HistidineHCAC,CAT
IsoleucineIATT,ATC,ATA
LysineKAAA,AAG
LeucineLTTG,CTT,TTA,CTA,CTC,CTG
MethionineMATG
AsparagineNAAT,AAC
ProlinePCCC,CCT,CCG,CCA
GlutamineQCAA,CAG
ArginineRAGG,CGT,AGA,CGC,CGG,CGA
SerineSTCT,AGT,TCA,AGC,TCC,TCG
ThreonineTACC,ACA,ACT,ACG
ValineVGTG,GTT,GTC,GTA
TryptophanWTGA,TGG
TyrosineYTAT,TAC
STOP*TAA,TAG