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/* (C) Copyright 1993-2006, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* gcode.h: Definitions for the translation of nucleotides to amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef __GCODE_H__
#define __GCODE_H__
typedef struct {
char *name;
char *code;
char *inits;
} GeneticCode, *GeneticCodePtr;
#define CODON_LEN 3 /* No. of nucleotides per codon */
#define NUMBER_OF_GENETIC_CODES 17
EXTERN GeneticCode gcodes[NUMBER_OF_GENETIC_CODES]
#ifdef INIT
= {
{"Standard",
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0001000000000000000100000000000000010000000000000000000000000000"},
{"Vertebrate Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
"0000000000000000000000000000000011110000000000000001000000000000"},
{"Yeast Mitochondrial",
"FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000110000000000000000000000000000"},
{"Mold Mitochondrial and Mycoplasma",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0011000000000000000100000000000011110000000000000001000000000000"},
{"Invertebrate Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
"0001000000000000000000000000000011110000000000000001000000000000"},
{"Ciliate Nuclear",
"FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Echinoderm Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000001000000000000"},
{"Euplotid Nuclear" ,
"FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Bacterial and Plant Plastid" ,
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0001000000000000000100000000000011110000000000000001000000000000"},
{"Alternative Yeast Nuclear" ,
"FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000100000000000000010000000000000000000000000000"},
{"Ascidian Mitochondrial" ,
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Flatworm Mitochondrial" ,
"FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Blepharisma Macronuclear" ,
"FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Chlorophycean Mitochondrial" ,
"FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Trematode Mitochondrial" ,
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000001000000000000"},
{"Scenedesmus obliquus mitochondrial" ,
"FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000"},
{"Thraustochytrium mitochondrial code" ,
"FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000010010000000000000001000000000000"}
}
#endif
;
void init_gcode PROTO((GeneticCodePtr, unsigned char [64], unsigned char [64]));
unsigned char codon2aa PROTO((unsigned char *, unsigned, unsigned, unsigned));
void aa2codon PROTO((unsigned char *));
#endif /* !__GCODE_H__ */
/* Change log information follows. */
/*
Changes since version 3.6:
10/14/04 fixed gcodes table (missing commas!)
Changes since version 3.4:
8/ 8/01 Updated from ncbi/data/gc.prt
Changes since version 3.1:
1/20/97 Added aa2codon()
*/
/* Old codes
"Protozoan Mitochondrial",
"FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0011000000000000000100000000000000010000000000000000000000000000",
"Plant Mitochondrial",
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRWIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
"0000000000000000000000000000000000010000000000000000000000000000",
*/
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