| 1 | #include <stdio.h> |
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| 2 | #include <stdlib.h> |
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| 3 | #include <math.h> |
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| 4 | #include "clustalw.h" |
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| 5 | |
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| 6 | #define MAX(a,b) ((a)>(b)?(a):(b)) |
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| 7 | #define MIN(a,b) ((a)<(b)?(a):(b)) |
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| 8 | |
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| 9 | /* |
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| 10 | * Prototypes |
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| 11 | */ |
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| 12 | |
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| 13 | static sint count_gaps(sint s1, sint s2, sint l); |
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| 14 | |
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| 15 | /* |
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| 16 | * Global Variables |
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| 17 | */ |
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| 18 | |
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| 19 | extern float gap_open; |
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| 20 | extern sint nseqs; |
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| 21 | extern sint *seqlen_array; |
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| 22 | extern short blosum45mt[]; |
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| 23 | extern short def_aa_xref[]; |
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| 24 | extern sint debug; |
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| 25 | extern sint max_aa; |
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| 26 | extern char **seq_array; |
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| 27 | |
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| 28 | |
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| 29 | void aln_score(void) |
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| 30 | { |
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| 31 | static short *mat_xref, *matptr; |
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| 32 | static sint maxres; |
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| 33 | static sint s1,s2,c1,c2; |
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| 34 | static sint ngaps; |
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| 35 | static sint i,l1,l2; |
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| 36 | static lint score; |
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| 37 | static sint matrix[NUMRES][NUMRES]; |
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| 38 | |
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| 39 | /* calculate an overall score for the alignment by summing the |
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| 40 | scores for each pairwise alignment */ |
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| 41 | |
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| 42 | matptr = blosum45mt; |
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| 43 | mat_xref = def_aa_xref; |
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| 44 | maxres = get_matrix(matptr, mat_xref, matrix, TRUE, 100); |
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| 45 | if (maxres == 0) |
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| 46 | { |
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| 47 | fprintf(stdout,"Error: matrix blosum30 not found\n"); |
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| 48 | return; |
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| 49 | } |
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| 50 | |
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| 51 | score=0; |
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| 52 | for (s1=1;s1<=nseqs;s1++) |
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| 53 | { |
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| 54 | for (s2=1;s2<s1;s2++) |
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| 55 | { |
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| 56 | |
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| 57 | l1 = seqlen_array[s1]; |
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| 58 | l2 = seqlen_array[s2]; |
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| 59 | for (i=1;i<l1 && i<l2;i++) |
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| 60 | { |
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| 61 | c1 = seq_array[s1][i]; |
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| 62 | c2 = seq_array[s2][i]; |
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| 63 | if ((c1>=0) && (c1<=max_aa) && (c2>=0) && (c2<=max_aa)) |
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| 64 | score += matrix[c1][c2]; |
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| 65 | } |
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| 66 | |
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| 67 | ngaps = count_gaps(s1, s2, l1); |
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| 68 | |
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| 69 | score -= 100 * gap_open * ngaps; |
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| 70 | |
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| 71 | } |
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| 72 | } |
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| 73 | |
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| 74 | score /= 100; |
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| 75 | |
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| 76 | info("Alignment Score %d", (pint)score); |
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| 77 | |
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| 78 | } |
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| 79 | |
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| 80 | static sint count_gaps(sint s1, sint s2, sint l) |
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| 81 | { |
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| 82 | sint i, g; |
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| 83 | sint q, r, *Q, *R; |
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| 84 | |
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| 85 | |
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| 86 | Q = (sint *)ckalloc((l+2) * sizeof(sint)); |
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| 87 | R = (sint *)ckalloc((l+2) * sizeof(sint)); |
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| 88 | |
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| 89 | Q[0] = R[0] = g = 0; |
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| 90 | |
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| 91 | for (i=1;i<l;i++) |
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| 92 | { |
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| 93 | if (seq_array[s1][i] > max_aa) q = 1; |
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| 94 | else q = 0; |
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| 95 | if (seq_array[s2][i] > max_aa) r = 1; |
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| 96 | else r = 0; |
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| 97 | |
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| 98 | if (((Q[i-1] <= R[i-1]) && (q != 0) && (1-r != 0)) || |
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| 99 | ((Q[i-1] >= R[i-1]) && (1-q != 0) && (r != 0))) |
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| 100 | g += 1; |
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| 101 | if (q != 0) Q[i] = Q[i-1]+1; |
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| 102 | else Q[i] = 0; |
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| 103 | |
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| 104 | if (r != 0) R[i] = R[i-1]+1; |
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| 105 | else R[i] = 0; |
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| 106 | } |
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| 107 | |
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| 108 | Q=ckfree((void *)Q); |
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| 109 | R=ckfree((void *)R); |
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| 110 | |
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| 111 | return(g); |
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| 112 | } |
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| 113 | |
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| 114 | |
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