--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* iupac.c
+ *
+ * Globally defines the IUPAC symbols for nucleic acid sequence
+ * Slowly evolving into a repository of globals. Tue Apr 20 1993
+ *
+ * RCS $Id: iupac.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: iupac.c,v 1.3 2001/02/21 21:09:10 eddy Exp)
+ */
+#include "squid.h"
+
+/* Default expected nucleotide occurrence frequencies, A/C/G/T.
+ * Used (for instance) as the default distribution for
+ * i.i.d. random nucleotide sequences.
+ */
+float dnafq[4] = { 0.25, 0.25, 0.25, 0.25 };
+
+/* Dayhoff f(i) amino acid occurrence frequencies.
+ * From SwissProt 34: 21,210,388 residues
+ * In alphabetic order by single-letter code.
+ * Used (for instance) as the default distribution for
+ * i.i.d. random protein sequences.
+ */
+float aafq[20] = {
+ 0.075520, /* A */
+ 0.016973, /* C */
+ 0.053029, /* D */
+ 0.063204, /* E */
+ 0.040762, /* F */
+ 0.068448, /* G */
+ 0.022406, /* H */
+ 0.057284, /* I */
+ 0.059398, /* K */
+ 0.093399, /* L */
+ 0.023569, /* M */
+ 0.045293, /* N */
+ 0.049262, /* P */
+ 0.040231, /* Q */
+ 0.051573, /* R */
+ 0.072214, /* S */
+ 0.057454, /* T */
+ 0.065252, /* V */
+ 0.012513, /* W */
+ 0.031985 /* Y */
+};
+
+char aa_alphabet[] = AMINO_ALPHABET;
+ /* aa_index converts to pam's 27x27 scheme */
+int aa_index[20] = { 0, 2, 3, 4, 5, 6, 7, 8, 10, 11,
+ 12, 13, 15, 16, 17, 18, 19, 21, 22, 24 };
+
+ /* IUPAC code translations */
+ /* note: sequence chars are UPPER CASE */
+struct iupactype iupac[] = {
+ { 'A', 'T', NTA, NTT, },
+ { 'C', 'G', NTC, NTG, },
+ { 'G', 'C', NTG, NTC, },
+ { 'T', 'A', NTT, NTA, },
+ { 'U', 'A', NTU, NTA, },
+ { 'N', 'N', NTN, NTN, },
+ { ' ', ' ', NTGAP, NTGAP, },
+ { 'R', 'Y', NTR, NTY, },
+ { 'Y', 'R', NTY, NTR, },
+ { 'M', 'K', NTM, NTK, },
+ { 'K', 'M', NTK, NTM, },
+ { 'S', 'S', NTS, NTS, },
+ { 'W', 'W', NTW, NTW, },
+ { 'H', 'D', NTH, NTD, },
+ { 'B', 'V', NTB, NTV, },
+ { 'V', 'B', NTV, NTB, },
+ { 'D', 'H', NTD, NTH, },
+ };
+
+
+char *stdcode1[65] = {
+ "K", /* AAA */
+ "N", /* AAC */
+ "K", /* AAG */
+ "N", /* AAU */
+ "T", /* ACA */
+ "T", /* ACC */
+ "T", /* ACG */
+ "T", /* ACU */
+ "R", /* AGA */
+ "S", /* AGC */
+ "R", /* AGG */
+ "S", /* AGU */
+ "I", /* AUA */
+ "I", /* AUC */
+ "M", /* AUG */
+ "I", /* AUU */
+ "Q", /* CAA */
+ "H", /* CAC */
+ "Q", /* CAG */
+ "H", /* CAU */
+ "P", /* CCA */
+ "P", /* CCC */
+ "P", /* CCG */
+ "P", /* CCU */
+ "R", /* CGA */
+ "R", /* CGC */
+ "R", /* CGG */
+ "R", /* CGU */
+ "L", /* CUA */
+ "L", /* CUC */
+ "L", /* CUG */
+ "L", /* CUU */
+ "E", /* GAA */
+ "D", /* GAC */
+ "E", /* GAG */
+ "D", /* GAU */
+ "A", /* GCA */
+ "A", /* GCC */
+ "A", /* GCG */
+ "A", /* GCU */
+ "G", /* GGA */
+ "G", /* GGC */
+ "G", /* GGG */
+ "G", /* GGU */
+ "V", /* GUA */
+ "V", /* GUC */
+ "V", /* GUG */
+ "V", /* GUU */
+ "*", /* UAA */
+ "Y", /* UAC */
+ "*", /* UAG */
+ "Y", /* UAU */
+ "S", /* UCA */
+ "S", /* UCC */
+ "S", /* UCG */
+ "S", /* UCU */
+ "*", /* UGA */
+ "C", /* UGC */
+ "W", /* UGG */
+ "C", /* UGU */
+ "L", /* UUA */
+ "F", /* UUC */
+ "L", /* UUG */
+ "F", /* UUU */
+ "X", /* unknown */
+};
+
+
+
+
+char *stdcode3[65] = {
+ "Lys", /* AAA */
+ "Asn", /* AAC */
+ "Lys", /* AAG */
+ "Asn", /* AAU */
+ "Thr", /* ACA */
+ "Thr", /* ACC */
+ "Thr", /* ACG */
+ "Thr", /* ACU */
+ "Arg", /* AGA */
+ "Ser", /* AGC */
+ "Arg", /* AGG */
+ "Ser", /* AGU */
+ "Ile", /* AUA */
+ "Ile", /* AUC */
+ "Met", /* AUG */
+ "Ile", /* AUU */
+ "Gln", /* CAA */
+ "His", /* CAC */
+ "Gln", /* CAG */
+ "His", /* CAU */
+ "Pro", /* CCA */
+ "Pro", /* CCC */
+ "Pro", /* CCG */
+ "Pro", /* CCU */
+ "Arg", /* CGA */
+ "Arg", /* CGC */
+ "Arg", /* CGG */
+ "Arg", /* CGU */
+ "Leu", /* CUA */
+ "Leu", /* CUC */
+ "Leu", /* CUG */
+ "Leu", /* CUU */
+ "Glu", /* GAA */
+ "Asp", /* GAC */
+ "Glu", /* GAG */
+ "Asp", /* GAU */
+ "Ala", /* GCA */
+ "Ala", /* GCC */
+ "Ala", /* GCG */
+ "Ala", /* GCU */
+ "Gly", /* GGA */
+ "Gly", /* GGC */
+ "Gly", /* GGG */
+ "Gly", /* GGU */
+ "Val", /* GUA */
+ "Val", /* GUC */
+ "Val", /* GUG */
+ "Val", /* GUU */
+ "***", /* UAA */
+ "Tyr", /* UAC */
+ "***", /* UAG */
+ "Tyr", /* UAU */
+ "Ser", /* UCA */
+ "Ser", /* UCC */
+ "Ser", /* UCG */
+ "Ser", /* UCU */
+ "***", /* UGA */
+ "Cys", /* UGC */
+ "Trp", /* UGG */
+ "Cys", /* UGU */
+ "Leu", /* UUA */
+ "Phe", /* UUC */
+ "Leu", /* UUG */
+ "Trp", /* UUU */
+ "XXX", /* unknown */
+};
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