128 lines
2.9 KiB
Plaintext
128 lines
2.9 KiB
Plaintext
/* 20-June-1986 universal pam file */
|
|
/* Changed by Rodger Staden and Simon Dear
|
|
** to suit local preferences 9-April-1992
|
|
*/
|
|
|
|
#ifndef XTERNAL
|
|
|
|
int gdelval= -1;
|
|
int ggapval= -4;
|
|
|
|
extern int gdelval, ggapval;
|
|
|
|
|
|
#define EOSEQ 127
|
|
#define MAXSQ 32
|
|
|
|
|
|
char sqnam[]={"aa"};
|
|
char sqtype[]={"protein"};
|
|
|
|
char *sq;
|
|
char aa[MAXSQ] = {"ARNDCQEGHILKMFPSTWYVBZX"};
|
|
|
|
int naa = 23;
|
|
int nsq;
|
|
|
|
int haa[MAXSQ] = {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,2,6,0};
|
|
int *hsq;
|
|
|
|
int apam[450] = {
|
|
2,
|
|
-2, 6,
|
|
0, 0, 2,
|
|
0,-1, 2, 4,
|
|
-2,-4,-4,-5,12,
|
|
0, 1, 1, 2,-5, 4,
|
|
0,-1, 1, 3,-5, 2, 4,
|
|
1,-3, 0, 1,-3,-1, 0, 5,
|
|
-1, 2, 2, 1,-3, 3, 1,-2, 6,
|
|
-1,-2,-2,-2,-2,-2,-2,-3,-2, 5,
|
|
-2,-3,-3,-4,-6,-2,-3,-4,-2, 2, 6,
|
|
-1, 3, 1, 0,-5, 1, 0,-2, 0,-2,-3, 5,
|
|
-1, 0,-2,-3,-5,-1,-2,-3,-2, 2, 4, 0, 6,
|
|
-4,-4,-4,-6,-4,-5,-5,-5,-2, 1, 2,-5, 0, 9,
|
|
1, 0,-1,-1,-3, 0,-1,-1, 0,-2,-3,-1,-2,-5, 6,
|
|
1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-3, 0,-2,-3, 1, 2,
|
|
1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-2, 0,-1,-3, 0, 1, 3,
|
|
-6, 2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4, 0,-6,-2,-5,17,
|
|
-3,-4,-2,-4, 0,-4,-4,-5, 0,-1,-1,-4,-2, 7,-5,-3,-3, 0,10,
|
|
0,-2,-2,-2,-2,-2,-2,-1,-2, 4, 2,-2, 2,-1,-1,-1, 0,-6,-2, 4,
|
|
0,-1, 2, 3,-4, 1, 2, 0, 1,-2,-3, 1,-2,-5,-1, 0, 0,-5,-3,-2, 2,
|
|
0, 0, 1, 3,-5, 3, 3,-1, 2,-2,-3, 0,-2,-5, 0, 0,-1,-6,-4,-2, 2, 3,
|
|
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
|
|
|
|
/* DNA alphabet
|
|
|
|
A, C, G, T U
|
|
R, Y
|
|
M (A or C) 6
|
|
W (A or T) 7
|
|
S (C or G) 8
|
|
K (G or T) 9
|
|
D (not C) 10
|
|
H (not G) 11
|
|
V (not T) 12
|
|
B (not A) 13
|
|
N X 14
|
|
*/
|
|
|
|
char nt[MAXSQ]={"ACGTURYMWSKDHVB-*"};
|
|
|
|
int nnt = 17;
|
|
|
|
int hnt[MAXSQ] = {0,1,2,3,3,0,1,0,0,1,2,0,0,0,1,0,0};
|
|
|
|
int npam[450] = {
|
|
/* A C G T U R Y M W S K D H V B - * */
|
|
4, /* A */
|
|
-3, 4, /* C */
|
|
-3,-3, 4, /* G */
|
|
-3,-3,-3, 4, /* T */
|
|
-3,-3,-3, 4, 4, /* U */
|
|
2,-1, 2,-1,-1, 2, /* R (A G)*/
|
|
-1, 2,-1, 2, 2,-2, 2, /* Y (C T)*/
|
|
2, 2,-1,-1,-1, 0, 0, 2, /* M (A C)*/
|
|
2,-1,-1, 2, 2, 1, 1, 1, 2, /* W (A T)*/
|
|
-1, 2, 2,-1,-1, 1, 1, 1,-1, 2, /* S (C G)*/
|
|
-1,-1, 2, 2, 2, 1, 1,-1, 1, 1, 2, /* K (G T)*/
|
|
1,-2, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, /* D (!C) */
|
|
1, 1,-2, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, /* H (!G) */
|
|
1, 1, 1,-2,-1, 1, 0, 1, 0, 1, 0, 0, 0, 1, /* V (!T) */
|
|
-2, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, /* B (!A) */
|
|
1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, /* - */
|
|
3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; /* * */
|
|
/* A C G T U R Y M W S K D H V B N */
|
|
|
|
int *pam;
|
|
int pam2[MAXSQ][MAXSQ];
|
|
int pamh1[MAXSQ]; /* used for kfact replacement */
|
|
|
|
#else
|
|
#define MAXSQ 32
|
|
|
|
extern char sqnam[];
|
|
extern char sqtype[];
|
|
extern int gdelval, ggapval;
|
|
extern char aa[];
|
|
extern char nt[];
|
|
extern char *sq;
|
|
|
|
#define EOSEQ 127
|
|
|
|
extern int naa;
|
|
extern int nnt;
|
|
extern int nsq;
|
|
|
|
extern int hnt[];
|
|
extern int haa[];
|
|
extern int *hsq;
|
|
|
|
extern int apam[];
|
|
extern int npam[];
|
|
extern int *pam;
|
|
|
|
extern int pam2[MAXSQ][MAXSQ];
|
|
extern int pamh1[];
|
|
#endif
|