PRIVATE double mfe_cost(const char *string, char *structure, const char *target)
{
#if TDIST
Tree *T1;
char *xstruc;
#endif
double energy, distance;
if (strlen(string)!=strlen(target)) {
fprintf(stderr, "%s\n%s\n", string, target);
nrerror("unequal length in mfe_cost");
}
energy = fold(string, structure);
#if TDIST
if (T0 == NULL) {
xstruc = expand_Full(target);
T0=make_tree(xstruc);
free(xstruc);
}
xstruc = expand_Full(structure);
T1=make_tree(xstruc);
distance = tree_edit_distance(T0,T1);
free(xstruc);
free_tree(T1);
#else
distance = (double) bp_distance(target, structure);
#endif
cost2 = energy_of_struct(string, target) - energy;
return (double) distance;
}
void main()
{
char *seq1="CGCAGGGAUACCCGCG", *seq2="GCGCCCAUAGGGACGC",
*struct1,* struct2,* xstruc;
float e1, e2, tree_dist, string_dist, profile_dist, kT;
Tree *T1, *T2;
swString *S1, *S2;
float *pf1, *pf2;
FLT_OR_DBL *bppm;
/* fold at 30C instead of the default 37C */
temperature = 30.; /* must be set *before* initializing */
/* allocate memory for structure and fold */
struct1 = (char* ) space(sizeof(char)*(strlen(seq1)+1));
e1 = fold(seq1, struct1);
struct2 = (char* ) space(sizeof(char)*(strlen(seq2)+1));
e2 = fold(seq2, struct2);
free_arrays(); /* free arrays used in fold() */
/* produce tree and string representations for comparison */
xstruc = expand_Full(struct1);
T1 = make_tree(xstruc);
S1 = Make_swString(xstruc);
free(xstruc);
xstruc = expand_Full(struct2);
T2 = make_tree(xstruc);
S2 = Make_swString(xstruc);
free(xstruc);
/* calculate tree edit distance and aligned structures with gaps */
edit_backtrack = 1;
tree_dist = tree_edit_distance(T1, T2);
free_tree(T1); free_tree(T2);
unexpand_aligned_F(aligned_line);
printf("%s\n%s %3.2f\n", aligned_line[0], aligned_line[1], tree_dist);
/* same thing using string edit (alignment) distance */
string_dist = string_edit_distance(S1, S2);
free(S1); free(S2);
printf("%s mfe=%5.2f\n%s mfe=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, string_dist);
/* for longer sequences one should also set a scaling factor for
partition function folding, e.g: */
kT = (temperature+273.15)*1.98717/1000.; /* kT in kcal/mol */
pf_scale = exp(-e1/kT/strlen(seq1));
/* calculate partition function and base pair probabilities */
e1 = pf_fold(seq1, struct1);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf1 = Make_bp_profile_bppm(bppm, strlen(seq1));
e2 = pf_fold(seq2, struct2);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf2 = Make_bp_profile_bppm(bppm, strlen(seq2));
free_pf_arrays(); /* free space allocated for pf_fold() */
profile_dist = profile_edit_distance(pf1, pf2);
printf("%s free energy=%5.2f\n%s free energy=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, profile_dist);
free_profile(pf1); free_profile(pf2);
}
