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/* File: iupac.h
* Author: Fred Wobus, 1999-08-26
* Copyright (c) 2010 - 2012 Genome Research Ltd
* ---------------------------------------------------------------------------
* SeqTools is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 3
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
* ---------------------------------------------------------------------------
* This file is part of the SeqTools sequence analysis package,
* written by
* Gemma Barson (Sanger Institute, UK) <gb10@sanger.ac.uk>
*
* based on original code by
* Erik Sonnhammer (SBC, Sweden) <Erik.Sonnhammer@sbc.su.se>
*
* and utilizing code taken from the AceDB and ZMap packages, written by
* Richard Durbin (Sanger Institute, UK) <rd@sanger.ac.uk>
* Jean Thierry-Mieg (CRBM du CNRS, France) <mieg@kaa.crbm.cnrs-mop.fr>
* Ed Griffiths (Sanger Institute, UK) <edgrif@sanger.ac.uk>
* Roy Storey (Sanger Institute, UK) <rds@sanger.ac.uk>
* Malcolm Hinsley (Sanger Institute, UK) <mh17@sanger.ac.uk>
*
* Description: Globally defines the IUPAC symbols for nucleic acid sequence
* iupac stuff from Sean Eddy's libsquid
*----------------------------------------------------------------------------
*/
#ifndef _iupac_h_included_
#define _iupac_h_included_
int PAM120[23][23] =
{
/*A R N D C Q E G H I L K M F P S T W Y V B Z X */
{ 3, -3, -1, 0, -3, -1, 0, 1, -3, -1, -3, -2, -2, -4, 1, 1, 1, -7, -4, 0, 1, 0, -1},
{-3, 6, -1, -3, -4, 1, -3, -4, 1, -2, -4, 2, -1, -5, -1, -1, -2, 1, -5, -3, -1, 0, -1},
{-1, -1, 4, 2, -5, 0, 1, 0, 2, -2, -4, 1, -3, -4, -2, 1, 0, -4, -2, -3, 4, 1, -1},
{ 0, -3, 2, 5, -7, 1, 3, 0, 0, -3, -5, -1, -4, -7, -3, 0, -1, -8, -5, -3, 5, 3, -1},
{-3, -4, -5, -7, 9, -7, -7, -4, -4, -3, -7, -7, -6, -6, -4, 0, -3, -8, -1, -3, -4, -6, -1},
{-1, 1, 0, 1, -7, 6, 2, -3, 3, -3, -2, 0, -1, -6, 0, -2, -2, -6, -5, -3, 1, 5, -1},
{ 0, -3, 1, 3, -7, 2, 5, -1, -1, -3, -4, -1, -3, -7, -2, -1, -2, -8, -5, -3, 3, 5, -1},
{ 1, -4, 0, 0, -4, -3, -1, 5, -4, -4, -5, -3, -4, -5, -2, 1, -1, -8, -6, -2, 1, -1, -1},
{-3, 1, 2, 0, -4, 3, -1, -4, 7, -4, -3, -2, -4, -3, -1, -2, -3, -3, -1, -3, 2, 2, -1},
{-1, -2, -2, -3, -3, -3, -3, -4, -4, 6, 1, -3, 1, 0, -3, -2, 0, -6, -2, 3, -2, -2, -1},
{-3, -4, -4, -5, -7, -2, -4, -5, -3, 1, 5, -4, 3, 0, -3, -4, -3, -3, -2, 1, -3, -2, -1},
{-2, 2, 1, -1, -7, 0, -1, -3, -2, -3, -4, 5, 0, -7, -2, -1, -1, -5, -5, -4, 1, 0, -1},
{-2, -1, -3, -4, -6, -1, -3, -4, -4, 1, 3, 0, 8, -1, -3, -2, -1, -6, -4, 1, -3, -1, -1},
{-4, -5, -4, -7, -6, -6, -7, -5, -3, 0, 0, -7, -1, 8, -5, -3, -4, -1, 4, -3, -4, -5, -1},
{ 1, -1, -2, -3, -4, 0, -2, -2, -1, -3, -3, -2, -3, -5, 6, 1, -1, -7, -6, -2, -1, 0, -1},
{ 1, -1, 1, 0, 0, -2, -1, 1, -2, -2, -4, -1, -2, -3, 1, 3, 2, -2, -3, -2, 1, 0, -1},
{ 1, -2, 0, -1, -3, -2, -2, -1, -3, 0, -3, -1, -1, -4, -1, 2, 4, -6, -3, 0, 1, -1, -1},
{-7, 1, -4, -8, -8, -6, -8, -8, -3, -6, -3, -5, -6, -1, -7, -2, -6, 12, -2, -8, -5, -6, -1},
{-4, -5, -2, -5, -1, -5, -5, -6, -1, -2, -2, -5, -4, 4, -6, -3, -3, -2, 8, -3, -2, -4, -1},
{ 0, -3, -3, -3, -3, -3, -3, -2, -3, 3, 1, -4, 1, -3, -2, -2, 0, -8, -3, 5, -2, -2, -1},
{ 1, -1, 4, 5, -4, 1, 3, 1, 2, -2, -3, 1, -3, -4, -1, 1, 1, -5, -2, -2, 6, 4, -1},
{ 0, 0, 1, 3, -6, 5, 5, -1, 2, -2, -2, 0, -1, -5, 0, 0, -1, -6, -4, -2, 4, 6, -1},
{-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}
};
#define NA 23 /* Not A residue - equal to X */
int aa_atob[] /* ASCII-to-binary translation table */
= {
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA, 1,21, 5, 4, 7,14, 8, 9,10,NA,12,11,13, 3,NA,
15, 6, 2,16,17,NA,20,18,23,19,22,NA,NA,NA,NA,NA,
NA, 1,21, 5, 4, 7,14, 8, 9,10,NA,12,11,13, 3,NA,
15, 6, 2,16,17,NA,20,18,23,19,22,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
};
struct iupactype
{
char sym; /* character representation */
char symcomp; /* complement (regular char */
char code; /* my binary rep */
char comp; /* binary encoded complement */
};
/* Binary encoding of the IUPAC code for nucleotides
*
* four-bit "word", permitting rapid degenerate matching
* A C G T/U
* 0 0 1 0
*/
#define NTA 8
#define NTC 4
#define NTG 2
#define NTT 1
#define NTU 1
#define NTN 15 /* A|C|G|T */
#define NTR 10 /* A|G */
#define NTY 5 /* C|T */
#define NTM 12 /* A|C */
#define NTK 3 /* G|T */
#define NTS 6 /* C|G */
#define NTW 9 /* A|T */
#define NTH 13 /* A|C|T */
#define NTB 7 /* C|G|T */
#define NTV 14 /* A|C|G */
#define NTD 11 /* A|G|T */
#define NTGAP 16 /* GAP */
#define NTEND 0 /* null string terminator */
/* ntmatch(): bitwise comparison of two nuc's */
/* note that it's sensitive to the order;
probe may be degenerate but target should
not be */
/* IUPAC code translations */
/* note: sequence chars are UPPER CASE */
/* in order of occurrence frequency;
to speed up loops a bit */
/* Define all of the valid characters in a DNA/RNA sequence, and their
* complements */
/* residue: inverse:
* A = adenine T
* C = cytosine G
* G = guanine C
* T = thymine (DNA only) A
* U = uracil (RNA only) A
* R = G/A (purine) Y = C/T
* Y = T/C (pyrimidine) R = G/A
* K = G/T (keto) M = C/A
* M = A/C (amino) K = T/G
* S = G/C (strong bonds) S = C/G
* W = A/T (weak bonds) W = T/A
* B = G/T/C (all but A) V = C/A/G
* D = G/A/T (all but C) H = C/T/A
* H = A/C/T (all but G) D = T/G/A
* V = G/C/A (all but T) B = C/G/T
* N = A/G/C/T (any) N = A/G/C/T
*/
#define IUPACSYMNUM 17
struct iupactype iupac[IUPACSYMNUM] =
{
{'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}
};
const 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 */
};
const 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 */
};
#endif /* _iupac_h_included_ */
|
