- static
- {
- /*
- * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- */
- ambiguityCodes.put("R", new String[] { "A", "G" });
- ambiguityCodes.put("Y", new String[] { "T", "C" });
- ambiguityCodes.put("W", new String[] { "A", "T" });
- ambiguityCodes.put("S", new String[] { "G", "C" });
- ambiguityCodes.put("M", new String[] { "A", "C" });
- ambiguityCodes.put("K", new String[] { "G", "T" });
- ambiguityCodes.put("H", new String[] { "A", "T", "C" });
- ambiguityCodes.put("B", new String[] { "G", "T", "C" });
- ambiguityCodes.put("V", new String[] { "G", "A", "C" });
- ambiguityCodes.put("D", new String[] { "G", "A", "T" });
- ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
-
- // Now build codon translation table
- codonHash2.put("AAA", "K");
- codonHash2.put("AAG", "K");
- codonHash2.put("AAC", "N");
- codonHash2.put("AAT", "N");
-
- codonHash2.put("CAA", "Q");
- codonHash2.put("CAG", "Q");
- codonHash2.put("CAC", "H");
- codonHash2.put("CAT", "H");
-
- codonHash2.put("GAA", "E");
- codonHash2.put("GAG", "E");
- codonHash2.put("GAC", "D");
- codonHash2.put("GAT", "D");
-
- codonHash2.put("TAC", "Y");
- codonHash2.put("TAT", "Y");
-
- codonHash2.put("ACA", "T");
- codonHash2.put("ACC", "T");
- codonHash2.put("ACT", "T");
- codonHash2.put("ACG", "T");
-
- codonHash2.put("CCA", "P");
- codonHash2.put("CCG", "P");
- codonHash2.put("CCC", "P");
- codonHash2.put("CCT", "P");
-
- codonHash2.put("GCA", "A");
- codonHash2.put("GCG", "A");
- codonHash2.put("GCC", "A");
- codonHash2.put("GCT", "A");
-
- codonHash2.put("TCA", "S");
- codonHash2.put("TCG", "S");
- codonHash2.put("TCC", "S");
- codonHash2.put("TCT", "S");
- codonHash2.put("AGC", "S");
- codonHash2.put("AGT", "S");
-
- codonHash2.put("AGA", "R");
- codonHash2.put("AGG", "R");
- codonHash2.put("CGA", "R");
- codonHash2.put("CGG", "R");
- codonHash2.put("CGC", "R");
- codonHash2.put("CGT", "R");
-
- codonHash2.put("GGA", "G");
- codonHash2.put("GGG", "G");
- codonHash2.put("GGC", "G");
- codonHash2.put("GGT", "G");
-
- codonHash2.put("TGA", "*");
- codonHash2.put("TAA", "*");
- codonHash2.put("TAG", "*");
-
- codonHash2.put("TGG", "W");
-
- codonHash2.put("TGC", "C");
- codonHash2.put("TGT", "C");
-
- codonHash2.put("ATA", "I");
- codonHash2.put("ATC", "I");
- codonHash2.put("ATT", "I");
-
- codonHash2.put("ATG", "M");
-
- codonHash2.put("CTA", "L");
- codonHash2.put("CTG", "L");
- codonHash2.put("CTC", "L");
- codonHash2.put("CTT", "L");
- codonHash2.put("TTA", "L");
- codonHash2.put("TTG", "L");
-
- codonHash2.put("GTA", "V");
- codonHash2.put("GTG", "V");
- codonHash2.put("GTC", "V");
- codonHash2.put("GTT", "V");
-
- codonHash2.put("TTC", "F");
- codonHash2.put("TTT", "F");
-
- buildAmbiguityCodonSet();
- }