Codon Usage Tools#

Configuration File: codon_usage_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the codon_usage_tools.json configuration file.

Available Tools#

CodonUsage_get_optimal_codons (Type: CodonUsageTool)#

Return the most-used codon for each amino acid in an organism, which is the reference table neede…

CodonUsage_get_optimal_codons tool specification

Tool Information:

  • Name: CodonUsage_get_optimal_codons

  • Type: CodonUsageTool

  • Description: Return the most-used codon for each amino acid in an organism, which is the reference table needed to codon-optimize a sequence for expression in that host. Example: taxid=83333 gives the preferred codons for E. coli K-12, which differ from human at ten amino acids. Use with DNA_codon_optimize when the target host is outside its four built-in species. Optimizing every position to the single best codon maximizes adaptation but can deplete tRNA pools, so the returned fraction supports proportional sampling instead.

Parameters:

  • taxid ([‘integer’, ‘string’]) (required) NCBI taxonomy identifier, e.g. 9606 (human) or 83333 (E. coli K-12).

  • include_stop_codons ([‘boolean’, ‘null’]) (optional) Include the stop codon group (reported as ‘End’). Default false.

Example Usage:

query = {
    "name": "CodonUsage_get_optimal_codons",
    "arguments": {
        "taxid": "example_value"
    }
}
result = tu.run(query)

CodonUsage_get_table (Type: CodonUsageTool)#

Retrieve the codon usage table for an organism from the Codon Usage Database, indexed by NCBI tax…

CodonUsage_get_table tool specification

Tool Information:

  • Name: CodonUsage_get_table

  • Type: CodonUsageTool

  • Description: Retrieve the codon usage table for an organism from the Codon Usage Database, indexed by NCBI taxonomy identifier. Returns all 64 codons with their raw count, frequency per thousand codons, and the fraction of their amino acid’s usage they account for. DNA_codon_optimize carries hardcoded tables for only four species; this supplies the reference data for any sequenced organism. Example: taxid=9606 for human, or taxid=9606 with amino_acid=’Leu’ for just the leucine codons.

Parameters:

  • taxid ([‘integer’, ‘string’]) (required) NCBI taxonomy identifier, e.g. 9606 (human), 83333 (E. coli K-12), 4932 (yeast), 7227 (fruit fly), 3702 (Arabidopsis). Tables are often held at strain level, so 562 for E. coli has no table but 83333 does.

  • amino_acid ([‘string’, ‘null’]) (optional) Restrict to one amino acid using its three-letter code, e.g. ‘Leu’, ‘Ala’, or ‘End’ for stop codons.

Example Usage:

query = {
    "name": "CodonUsage_get_table",
    "arguments": {
        "taxid": "example_value"
    }
}
result = tu.run(query)