@aleph-ai/tinyaleph 1.2.0 → 1.3.0

package/backends/bioinformatics/genetic-code.js

@@ -0,0 +1,269 @@
+/**
+ * Genetic Code - Codon to Amino Acid Translation
+ * 
+ * The universal genetic code mapping 64 codons to 20 amino acids + stop.
+ * Also includes alternative genetic codes for mitochondria and other organisms.
+ */
+
+// ============================================================================
+// Standard Genetic Code
+// ============================================================================
+
+/**
+ * Standard (universal) genetic code
+ * Maps RNA codons to single-letter amino acid codes
+ */
+const STANDARD_GENETIC_CODE = {
+  // UUX codons
+  'UUU': 'F', 'UUC': 'F',  // Phenylalanine
+  'UUA': 'L', 'UUG': 'L',  // Leucine
+  
+  // UCX codons
+  'UCU': 'S', 'UCC': 'S', 'UCA': 'S', 'UCG': 'S',  // Serine
+  
+  // UAX codons
+  'UAU': 'Y', 'UAC': 'Y',  // Tyrosine
+  'UAA': '*', 'UAG': '*',  // Stop (Ochre, Amber)
+  
+  // UGX codons
+  'UGU': 'C', 'UGC': 'C',  // Cysteine
+  'UGA': '*',              // Stop (Opal)
+  'UGG': 'W',              // Tryptophan
+  
+  // CUX codons
+  'CUU': 'L', 'CUC': 'L', 'CUA': 'L', 'CUG': 'L',  // Leucine
+  
+  // CCX codons
+  'CCU': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',  // Proline
+  
+  // CAX codons
+  'CAU': 'H', 'CAC': 'H',  // Histidine
+  'CAA': 'Q', 'CAG': 'Q',  // Glutamine
+  
+  // CGX codons
+  'CGU': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',  // Arginine
+  
+  // AUX codons
+  'AUU': 'I', 'AUC': 'I', 'AUA': 'I',  // Isoleucine
+  'AUG': 'M',                           // Methionine (START)
+  
+  // ACX codons
+  'ACU': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',  // Threonine
+  
+  // AAX codons
+  'AAU': 'N', 'AAC': 'N',  // Asparagine
+  'AAA': 'K', 'AAG': 'K',  // Lysine
+  
+  // AGX codons
+  'AGU': 'S', 'AGC': 'S',  // Serine
+  'AGA': 'R', 'AGG': 'R',  // Arginine
+  
+  // GUX codons
+  'GUU': 'V', 'GUC': 'V', 'GUA': 'V', 'GUG': 'V',  // Valine
+  
+  // GCX codons
+  'GCU': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',  // Alanine
+  
+  // GAX codons
+  'GAU': 'D', 'GAC': 'D',  // Aspartic acid
+  'GAA': 'E', 'GAG': 'E',  // Glutamic acid
+  
+  // GGX codons
+  'GGU': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G',  // Glycine
+};
+
+/**
+ * Vertebrate mitochondrial genetic code
+ * Differs from standard in UGA=W, AGA/AGG=*, AUA=M
+ */
+const VERTEBRATE_MITOCHONDRIAL_CODE = {
+  ...STANDARD_GENETIC_CODE,
+  'UGA': 'W',  // Tryptophan instead of Stop
+  'AGA': '*',  // Stop instead of Arginine
+  'AGG': '*',  // Stop instead of Arginine
+  'AUA': 'M',  // Methionine instead of Isoleucine
+};
+
+/**
+ * Yeast mitochondrial genetic code
+ */
+const YEAST_MITOCHONDRIAL_CODE = {
+  ...STANDARD_GENETIC_CODE,
+  'UGA': 'W',
+  'CUU': 'T', 'CUC': 'T', 'CUA': 'T', 'CUG': 'T',  // Threonine
+  'AUA': 'M',
+};
+
+// ============================================================================
+// Codon Properties
+// ============================================================================
+
+/**
+ * Start codons by genetic code
+ */
+const START_CODONS = {
+  standard: ['AUG'],
+  vertebrate_mitochondrial: ['AUG', 'AUA', 'AUU'],
+  bacterial: ['AUG', 'GUG', 'UUG'],
+};
+
+/**
+ * Stop codons by genetic code
+ */
+const STOP_CODONS = {
+  standard: ['UAA', 'UAG', 'UGA'],
+  vertebrate_mitochondrial: ['UAA', 'UAG', 'AGA', 'AGG'],
+};
+
+/**
+ * Codon usage frequency table (E. coli)
+ * Values are relative frequencies (0-1)
+ */
+const CODON_USAGE_ECOLI = {
+  'UUU': 0.58, 'UUC': 0.42, 'UUA': 0.14, 'UUG': 0.13,
+  'UCU': 0.17, 'UCC': 0.15, 'UCA': 0.14, 'UCG': 0.14,
+  'UAU': 0.59, 'UAC': 0.41, 'UAA': 0.61, 'UAG': 0.09,
+  'UGU': 0.46, 'UGC': 0.54, 'UGA': 0.30, 'UGG': 1.00,
+  'CUU': 0.12, 'CUC': 0.10, 'CUA': 0.04, 'CUG': 0.47,
+  'CCU': 0.18, 'CCC': 0.13, 'CCA': 0.20, 'CCG': 0.49,
+  'CAU': 0.57, 'CAC': 0.43, 'CAA': 0.34, 'CAG': 0.66,
+  'CGU': 0.36, 'CGC': 0.36, 'CGA': 0.07, 'CGG': 0.11,
+  'AUU': 0.49, 'AUC': 0.39, 'AUA': 0.11, 'AUG': 1.00,
+  'ACU': 0.19, 'ACC': 0.40, 'ACA': 0.17, 'ACG': 0.25,
+  'AAU': 0.49, 'AAC': 0.51, 'AAA': 0.74, 'AAG': 0.26,
+  'AGU': 0.16, 'AGC': 0.25, 'AGA': 0.07, 'AGG': 0.04,
+  'GUU': 0.28, 'GUC': 0.20, 'GUA': 0.15, 'GUG': 0.37,
+  'GCU': 0.18, 'GCC': 0.26, 'GCA': 0.23, 'GCG': 0.33,
+  'GAU': 0.63, 'GAC': 0.37, 'GAA': 0.68, 'GAG': 0.32,
+  'GGU': 0.35, 'GGC': 0.37, 'GGA': 0.13, 'GGG': 0.15,
+};
+
+// ============================================================================
+// Codon Functions
+// ============================================================================
+
+/**
+ * Get amino acid from codon
+ */
+function translateCodon(codon, geneticCode = STANDARD_GENETIC_CODE) {
+  const normalized = codon.toUpperCase().replace(/T/g, 'U');
+  return geneticCode[normalized] || '?';
+}
+
+/**
+ * Get all codons for an amino acid (degeneracy)
+ */
+function getCodonsForAminoAcid(aa, geneticCode = STANDARD_GENETIC_CODE) {
+  return Object.entries(geneticCode)
+    .filter(([_, aminoAcid]) => aminoAcid === aa.toUpperCase())
+    .map(([codon, _]) => codon);
+}
+
+/**
+ * Get degeneracy (number of codons) for amino acid
+ */
+function getCodonDegeneracy(aa, geneticCode = STANDARD_GENETIC_CODE) {
+  return getCodonsForAminoAcid(aa, geneticCode).length;
+}
+
+/**
+ * Check if codon is a start codon
+ */
+function isStartCodon(codon, codeType = 'standard') {
+  const normalized = codon.toUpperCase().replace(/T/g, 'U');
+  return START_CODONS[codeType]?.includes(normalized) || false;
+}
+
+/**
+ * Check if codon is a stop codon
+ */
+function isStopCodon(codon, geneticCode = STANDARD_GENETIC_CODE) {
+  const normalized = codon.toUpperCase().replace(/T/g, 'U');
+  return geneticCode[normalized] === '*';
+}
+
+/**
+ * Calculate GC content of a sequence
+ */
+function calculateGCContent(sequence) {
+  const clean = sequence.toUpperCase();
+  const gc = (clean.match(/[GC]/g) || []).length;
+  return gc / clean.length;
+}
+
+/**
+ * Calculate codon adaptation index (CAI)
+ */
+function calculateCAI(sequence, usageTable = CODON_USAGE_ECOLI) {
+  const codons = [];
+  const rna = sequence.toUpperCase().replace(/T/g, 'U');
+  
+  for (let i = 0; i < rna.length - 2; i += 3) {
+    codons.push(rna.slice(i, i + 3));
+  }
+  
+  // Calculate geometric mean of relative adaptiveness
+  let sumLog = 0;
+  let count = 0;
+  
+  for (const codon of codons) {
+    const freq = usageTable[codon];
+    if (freq && freq > 0) {
+      sumLog += Math.log(freq);
+      count++;
+    }
+  }
+  
+  return count > 0 ? Math.exp(sumLog / count) : 0;
+}
+
+/**
+ * Synonymous codon substitution possibilities
+ */
+function getSynonymousCodons(codon, geneticCode = STANDARD_GENETIC_CODE) {
+  const aa = translateCodon(codon, geneticCode);
+  if (aa === '?' || aa === '*') return [];
+  
+  return getCodonsForAminoAcid(aa, geneticCode)
+    .filter(c => c !== codon.toUpperCase().replace(/T/g, 'U'));
+}
+
+/**
+ * Classify mutation effect
+ */
+function classifyMutation(originalCodon, mutatedCodon, geneticCode = STANDARD_GENETIC_CODE) {
+  const original = originalCodon.toUpperCase().replace(/T/g, 'U');
+  const mutated = mutatedCodon.toUpperCase().replace(/T/g, 'U');
+  
+  const originalAA = geneticCode[original];
+  const mutatedAA = geneticCode[mutated];
+  
+  if (!originalAA || !mutatedAA) return 'unknown';
+  if (originalAA === mutatedAA) return 'synonymous';
+  if (mutatedAA === '*') return 'nonsense';
+  if (originalAA === '*') return 'readthrough';
+  return 'missense';
+}
+
+module.exports = {
+  // Genetic codes
+  STANDARD_GENETIC_CODE,
+  VERTEBRATE_MITOCHONDRIAL_CODE,
+  YEAST_MITOCHONDRIAL_CODE,
+  
+  // Codon lists
+  START_CODONS,
+  STOP_CODONS,
+  CODON_USAGE_ECOLI,
+  
+  // Functions
+  translateCodon,
+  getCodonsForAminoAcid,
+  getCodonDegeneracy,
+  isStartCodon,
+  isStopCodon,
+  calculateGCContent,
+  calculateCAI,
+  getSynonymousCodons,
+  classifyMutation,
+};