Benchling · Schema

OptimizeCodons

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Properties

Name	Type	Description
avoidedCutsiteEnzymeIds	array	List of enzyme IDs whose recognition sites will be avoided when creating the optimized sequence.
codonUsageTableId	string	ID of the codon usage table representing the target organism.
dnaSequenceIds	array	IDs of DNA sequences to codon-optimize.
folderId	string	ID of the folder in which the optimized sequences will be saved.
gcContent	string	The amount of GC content in the optimized sequence. LOW is defined as below 0.33, MEDIUM as 0.33-0.66, and HIGH as above 0.66. If neither gcContent nor gcContentRange is specified, the optimization wi
gcContentRange	object	Custom GC content range for the optimized sequence, specified as decimal values between 0 and 1. The maximum must be greater than the minimum. Cannot be specified together with gcContent.
hairpinParameters	object	These parameters are applied in the AvoidHairpins specification in DNAChisel. If hairpinParameters is not specified, hairpins will not be avoided.
method	string	The codon optimization algorithm to use. Requires codonUsageTableId to be specified. MATCH_CODON_USAGE selects codons probabilistically based on the organism's codon usage frequencies. USE_BEST_CODON
reducedPatterns	array	List of patterns to avoid when creating the optimized sequence, on the coding strand only.
schemaId	string	ID of the optimized DNA sequences' schemas
shouldDepleteUridine	boolean	If not specified, the optimization will default to false, and mRNA uridine depletion will not be performed.

View JSON Schema on GitHub

JSON Schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://api-evangelist.github.io/benchling/json-schema/OptimizeCodons.json",
  "title": "OptimizeCodons",
  "additionalProperties": false,
  "properties": {
    "avoidedCutsiteEnzymeIds": {
      "description": "List of enzyme IDs whose recognition sites will be avoided when creating the optimized sequence.\n",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "codonUsageTableId": {
      "description": "ID of the codon usage table representing the target organism.",
      "type": "string"
    },
    "dnaSequenceIds": {
      "description": "IDs of DNA sequences to codon-optimize.",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "folderId": {
      "description": "ID of the folder in which the optimized sequences will be saved.\n",
      "type": "string"
    },
    "gcContent": {
      "default": "ANY",
      "description": "The amount of GC content in the optimized sequence. LOW is defined as below 0.33, MEDIUM as 0.33-0.66, and HIGH as above 0.66. If neither gcContent nor gcContentRange is specified, the optimization will default to ANY (0-1). Cannot be specified together with gcContentRange.\n",
      "enum": [
        "ANY",
        "LOW",
        "MEDIUM",
        "HIGH"
      ],
      "type": "string"
    },
    "gcContentRange": {
      "additionalProperties": false,
      "description": "Custom GC content range for the optimized sequence, specified as decimal values between 0 and 1. The maximum must be greater than the minimum. Cannot be specified together with gcContent.\n",
      "properties": {
        "max": {
          "description": "Maximum GC content ratio (e.g., 0.6 for 60%)",
          "maximum": 1,
          "minimum": 0,
          "type": "number"
        },
        "min": {
          "description": "Minimum GC content ratio (e.g., 0.4 for 40%)",
          "maximum": 1,
          "minimum": 0,
          "type": "number"
        }
      },
      "type": "object"
    },
    "hairpinParameters": {
      "additionalProperties": false,
      "description": "These parameters are applied in the AvoidHairpins specification in DNAChisel. If hairpinParameters is not specified, hairpins will not be avoided.\n",
      "properties": {
        "stem": {
          "default": 20,
          "type": "integer"
        },
        "window": {
          "default": 200,
          "type": "integer"
        }
      },
      "type": "object"
    },
    "method": {
      "default": "MATCH_CODON_USAGE",
      "description": "The codon optimization algorithm to use. Requires codonUsageTableId to be specified. MATCH_CODON_USAGE selects codons probabilistically based on the organism's codon usage frequencies. USE_BEST_CODON always selects the most frequently used codon for each amino acid.\n",
      "enum": [
        "MATCH_CODON_USAGE",
        "USE_BEST_CODON"
      ],
      "type": "string"
    },
    "reducedPatterns": {
      "description": "List of patterns to avoid when creating the optimized sequence, on the coding strand only.\n",
      "items": {
        "$ref": "#/components/schemas/ReducedPattern"
      },
      "type": "array"
    },
    "schemaId": {
      "description": "ID of the optimized DNA sequences' schemas",
      "type": "string"
    },
    "shouldDepleteUridine": {
      "default": false,
      "description": "If not specified, the optimization will default to false, and mRNA uridine depletion will not be performed.\n",
      "type": "boolean"
    }
  },
  "required": [
    "dnaSequenceIds",
    "folderId"
  ],
  "type": "object"
}