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()
Code ID | Name |
---|---|
1 | Standard |
2 | Vertebrate Mitochondrial |
3 | Yeast Mitochondrial |
4 | Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma |
5 | Invertebrate Mitochondrial |
6 | Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear |
9 | Echinoderm Mitochondrial; Flatworm Mitochondrial |
10 | Euplotid Nuclear |
11 | Bacterial, Archaeal and Plant Plastid |
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 | Rhabdopleuridae Mitochondrial |
25 | Candidate Division SR1 and Gracilibacteria |
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 |
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
aa | IUPAC code | codons |
---|---|---|
Alanine | A | GCG,GCC,GCT,GCA |
Cysteine | C | TGT,TGC |
Aspartic Acid | D | GAT,GAC |
Glutamic Acid | E | GAG,GAA |
Phenylalanine | F | TTC,TTT |
Glycine | G | GGG,GGA,GGC,GGT |
Histidine | H | CAT,CAC |
Isoleucine | I | ATT,ATA,ATC |
Lysine | K | AAG,AAA |
Leucine | L | CTG,TTG,CTC,TTA,CTT,CTA |
Methionine | M | ATG |
Asparagine | N | AAC,AAT |
Proline | P | CCA,CCC,CCG,CCT |
Glutamine | Q | CAA,CAG |
Arginine | R | CGC,CGT,CGG,AGA,CGA,AGG |
Serine | S | TCC,AGC,TCT,TCG,TCA,AGT |
Threonine | T | ACT,ACA,ACC,ACG |
Valine | V | GTT,GTG,GTC,GTA |
Tryptophan | W | TGA,TGG |
Tyrosine | Y | TAC,TAT |
STOP | * | TAA,TAG |