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/* (C) Copyright 1993-9, 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.c: Functions for the translation of nucleotides to amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */
#include <global.h>
#include <residues.h>
#include <sequences.h>
/* ----------------------- initialize a genetic code -------------------*/
void
init_gcode(gp, xltab, rcxltab)
GeneticCodePtr gp;
register unsigned char xltab[64], rcxltab[64];
{
register char *code;
register int i, j, k, tot;
/* gctrans -- used to translate from the binary alphabet used in ntbet.h
into a binary alphabet appropriate for the GeneticCode strings */
static unsigned char gctrans[] = { '\003', '\001', '\000', '\002' };
code = gp->code;
for (i=0; i<4; ++i) {
for (j=0; j<4; ++j) {
for (k=0; k<4; ++k, ++code) {
tot = gctrans[i]*4*4 + gctrans[j]*4 + gctrans[k];
xltab[tot] = aa_atob[(int)*code];
tot = (3-gctrans[i])*4*4 + (3-gctrans[j])*4 + (3-gctrans[k]);
rcxltab[tot] = aa_atob[(int)*code];
}
}
}
return;
}
/*
codon2aa
Translate 3 binary-encoded nucleotides (n1, n2, and n3) into a binary
amino acid in the specified genetic code.
*/
unsigned char
codon2aa(gcode, n1, n2, n3)
unsigned char *gcode;
unsigned n1, n2, n3;
{
if (n1 < 4 && n2 < 4 && n3 < 4)
return gcode[n1*4*4 + n2*4 + n3];
if (n1 >= NUCID_MAX || n2 >= NUCID_MAX || n3 >= NUCID_MAX)
return (unsigned char)aa_atob[UNKNOWN_AA_CHR];
{
unsigned char aa;
unsigned char b1, b2, b3;
int i1, i2, i3;
b1 = nt_bdegen[n1].list[0];
b2 = nt_bdegen[n2].list[0];
b3 = nt_bdegen[n3].list[0];
aa = gcode[b1*4*4 + b2*4 + b3];
for (i1=0; i1 < nt_bdegen[n1].ndegen; ++i1) {
b1 = nt_bdegen[n1].list[i1]*4*4;
for (i2=0; i2 < nt_bdegen[n2].ndegen; ++i2) {
b2 = b1 + nt_bdegen[n2].list[i2]*4;
for (i3=0; i3 < nt_bdegen[n3].ndegen; ++i3) {
b3 = nt_bdegen[n3].list[i3];
if (gcode[b2 + b3] != aa)
return (unsigned char)aa_atob[UNKNOWN_AA_CHR];
}
}
}
return aa;
}
/*NOTREACHED*/
} /* end of codon2aa */
/*
aa2codon
Translate a single binary-encoded amino acid into 3 binary-encoded
nucleotides (n1, n2, and n3)
Note: Could add translation tables to gcode.h
The translations here are simplified to one degenerate codon per aa
and therefore not quite correct for:
Arg (R) = CGT, CGC, CGA, CGG; AGA, AGG = CGN or AGR
Leu (L) = CTT, CTC, CTA, CTG; TTA, TTG = CTN or TTR
Ser (S) = TCT, TCC, TCA, TCG; AGT, AGC = TCN or AGY
*/
void aa2codon(aa, n1, n2, n3)
Residue aa, *n1, *n2, *n3;
{
switch (aa)
{
case 0: /* - => --- */
{ *n1 = *n2 = *n3 = nt_atob['-']; }
break;
case 1: /* A => GCN */
{ *n1 = nt_atob['G']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
break;
case 2: /* R => MGN */
{ *n1 = nt_atob['M']; *n2 = nt_atob['G']; *n3 = nt_atob['N']; }
break;
case 3: /* N => AAY */
{ *n1 = nt_atob['A']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
break;
case 4: /* D => GAY */
{ *n1 = nt_atob['G']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
break;
case 5: /* C => UGY */
{ *n1 = nt_atob['U']; *n2 = nt_atob['G']; *n3 = nt_atob['Y']; }
break;
case 6: /* Q => CAR */
{ *n1 = nt_atob['C']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
break;
case 7: /* E => GAR */
{ *n1 = nt_atob['G']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
break;
case 8: /* G => GGN */
{ *n1 = nt_atob['G']; *n2 = nt_atob['G']; *n3 = nt_atob['N']; }
break;
case 9: /* H => CAY */
{ *n1 = nt_atob['C']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
break;
case 10: /* I => ATH */
{ *n1 = nt_atob['A']; *n2 = nt_atob['T']; *n3 = nt_atob['H']; }
break;
case 11: /* L => YTN */
{ *n1 = nt_atob['Y']; *n2 = nt_atob['T']; *n3 = nt_atob['N']; }
break;
case 12: /* K => AAR */
{ *n1 = nt_atob['A']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
break;
case 13: /* M => ATG */
{ *n1 = nt_atob['A']; *n2 = nt_atob['T']; *n3 = nt_atob['G']; }
break;
case 14: /* F => TTY */
{ *n1 = nt_atob['T']; *n2 = nt_atob['T']; *n3 = nt_atob['Y']; }
break;
case 15: /* P => CCN */
{ *n1 = nt_atob['C']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
break;
case 16: /* S => WSN */
{ *n1 = nt_atob['W']; *n2 = nt_atob['S']; *n3 = nt_atob['N']; }
break;
case 17: /* T => ACN */
{ *n1 = nt_atob['A']; *n2 = nt_atob['C']; *n3 = nt_atob['N']; }
break;
case 18: /* W => TGG */
{ *n1 = nt_atob['T']; *n2 = nt_atob['G']; *n3 = nt_atob['G']; }
break;
case 19: /* Y => TAY */
{ *n1 = nt_atob['T']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
break;
case 20: /* V => GTN */
{ *n1 = nt_atob['G']; *n2 = nt_atob['T']; *n3 = nt_atob['N']; }
break;
case 21: /* B (D or N) => RAY */
{ *n1 = nt_atob['R']; *n2 = nt_atob['A']; *n3 = nt_atob['Y']; }
break;
case 22: /* Z (E or Q) => SAR */
{ *n1 = nt_atob['S']; *n2 = nt_atob['A']; *n3 = nt_atob['R']; }
break;
case 23: /* X => NNN */
{ *n1 = nt_atob['N']; *n2 = nt_atob['N']; *n3 = nt_atob['N']; }
break;
case 24: /* * => TRR (stop) */
{ *n1 = nt_atob['T']; *n2 = nt_atob['R']; *n3 = nt_atob['R']; }
break;
default: /* Unknown */
{ *n1 = nt_atob['N']; *n2 = nt_atob['N']; *n3 = nt_atob['N']; }
break;
}
} /* end of aa2codon */
/* Change log information follows. */
/* Changes since Blimps Version 3.1:
* 1/19/1997 Added aa2codon() routine.
*
*/
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