Available genetic codes#
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,GCT,GCA,GCC |
| Cysteine | C | TGT,TGC |
| Aspartic Acid | D | GAT,GAC |
| Glutamic Acid | E | GAA,GAG |
| Phenylalanine | F | TTC,TTT |
| Glycine | G | GGC,GGG,GGA,GGT |
| Histidine | H | CAC,CAT |
| Isoleucine | I | ATA,ATT,ATC |
| Lysine | K | AAA,AAG |
| Leucine | L | CTC,TTA,CTT,CTG,TTG,CTA |
| Methionine | M | ATG |
| Asparagine | N | AAC,AAT |
| Proline | P | CCC,CCG,CCT,CCA |
| Glutamine | Q | CAA,CAG |
| Arginine | R | AGA,CGG,CGT,CGC,CGA,AGG |
| Serine | S | TCC,TCG,TCA,AGT,TCT,AGC |
| Threonine | T | ACT,ACA,ACG,ACC |
| Valine | V | GTT,GTC,GTA,GTG |
| Tryptophan | W | TGG,TGA |
| Tyrosine | Y | TAC,TAT |
| STOP | * | TAA,TAG |