Codon Synonymous Site Mask Tool

Description

Mark neighbors matching its nonexcluded amino-acid token and sum their weights by changed position and overall.

Sequence-derived quantities depend on aligned observations, callable sites and a stated substitution or codon model. A count ratio or one site's opportunity is distinct from a corrected evolutionary distance or statistical evidence of selection.

Mark neighbors matching its nonexcluded amino-acid token and sum their weights by changed position and overall.

When to use this tool

Use Codon Synonymous Site Mask when you need the stated sequence-distance or codon-opportunity term.

How to use the tool and how it works

Enter codon, codeCodons, aminoAcids, neighborCodons, neighborWeights, excludedAminoAcidTokens. Keep parallel arrays aligned. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read synonymousMask, siteOpportunity, totalOpportunity. Use the output convention below.

Require a supplied unique uppercase-DNA codon map and aligned unique one-base neighbors/weights, with a mapped nonexcluded focal codon. Mark neighbors matching its nonexcluded amino-acid token and sum their weights by changed position and overall.^[1]

Input field	Meaning and units	Accepted input
codon	Codon	Required. Text; maximum UTF-16 length 8192.
codeCodons	Code Codons	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
aminoAcids	Amino Acids	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
neighborCodons	Neighbor Codons	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
neighborWeights	Neighbor Weights	Required. Array of finite number; minimum 0; maximum items 256.
excludedAminoAcidTokens	Excluded Amino Acid Tokens	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.

Output field	Interpretation	Returned shape
synonymousMask	Synonymous Mask	Required. Array of boolean; maximum items 256.
siteOpportunity	Three sums of synonymous neighbor weights by changed zero-based codon position, not necessarily standard normalized site counts.	Required. Array of finite number; maximum items 256.
totalOpportunity	Total Opportunity	Required. Finite number.

json

{
  "input": {
    "codon": "GCT",
    "codeCodons": [
      "GCT",
      "GCC",
      "GAT"
    ],
    "aminoAcids": [
      "A",
      "A",
      "D"
    ],
    "neighborCodons": [
      "GCC",
      "GAT"
    ],
    "neighborWeights": [
      0.5,
      0.5
    ],
    "excludedAminoAcidTokens": [
      "*"
    ]
  },
  "output": {
    "synonymousMask": [
      true,
      false
    ],
    "siteOpportunity": [
      0,
      0,
      0.5
    ],
    "totalOpportunity": 0.5
  }
}

Limitations and assumptions

The genetic code and excluded tokens are caller supplied; neighbor opportunities need not cover all mutations or sum to standard site counts. No default genetic code or complete dN/dS estimate is inferred.
Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.

Alternative or Complementary methods

Use a complete sequence-analysis method with an appropriate alignment, genetic code and model. Review gaps, missingness, multiple substitutions, saturation and uncertainty before biological interpretation.

References

Calculation and input contract: evolutionary-biology/codon-synonymous-site-mask — tool.io

Similar or alternative tools

Codon Site Opportunity Share
Sum callable opportunities and selected callable opportunity; divide or return flagged zero.
dN/dS One Codon Site Count Term
Return change/site dN and dS and their ratio.