OptimiseDNACodons

apiblocks.OptimiseDNACodons

Optimises the coding sequence for expression in a target organism or according to the supplied codon table. If both are given, the supplied codon table will be used.

Use best codon (use_best_codon)

This method will substitute codons for the most used one in the target table or organism.

Match codon usage (match_codon_usage)

This method will substitute codons probabilistically, emulating the usage of the codons in the taget table or organism.

Parameters:

Name	Type	Description	Example	Default
method	Optional[Literal['use_best_codon', 'match_codon_usage']]	Custom codon table for the optimisation	"match_codon_usage"	"match_codon_usage"
dna	DNA	Target DNA sequence to optimise	{ "seq": "ATGTTAGAG" }
organism	Optional[Organism]	Target organism for the optimisation	{ "name": "e_coli", "tax_id": 316407 }
codon_table	Optional[CodonTable]	Custom codon table for the optimisation		null

Returns:

Type	Description
DNA	Codon optimised DNA.

Raises:

Type	Description
Codon table not found	If a codon table for the given organism is not found.

Available tables

Organism name	Tax id
b_subtilis	1423
d_melanogaster	7227
m_musculus_domesticus	10092
m_musculus	10090
e_coli	316407
g_gallus	9031
c_elegans	6239
s_cerevisiae	4932
h_sapiens	9606

References

DNA Chisel - a versatile sequence optimizer

codon-usage-tables

Examples:

$ curl 'https://api.apiblocks.dev/rpc' \
-H 'X-API-KEY: $APIBLOCKS_TOKEN' \
-H 'Content-Type: application/json' \
--data '{
    "id": "c233218b-46c8-471d-b65f-2cd16ab47ebe",
    "method": "apiblocks.OptimiseDNACodons",
    "params": {
      "method": "match_codon_usage",
      "dna": {
        "seq": "ATGTTAGAG"
      },
      "organism": {
        "name": "e_coli",
        "tax_id": 316407
      }
    }
  }'