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iupac.c

/*****************************************************************
 * HMMER - Biological sequence analysis with profile HMMs
 * Copyright (C) 1992-1998 Washington University School of Medicine
 * All Rights Reserved
 * 
 *     This source code is distributed under the terms of the
 *     GNU General Public License. See the files COPYING 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,v 1.2 1998/10/09 18:07:16 eddy Exp $
 */
#include "squid.h"

#ifdef MEMDEBUG
#include "dbmalloc.h"
#endif

char squid_version[] = "1.5m";
char squid_date[]    = "Sept 1997";

/* Dayhoff f(i) amino acid occurrence frequencies. 
 * From SwissProt 34: 21,210,388 residues
 * In alphabetic order by single-letter code.
 */
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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