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bm4321_sequence_alignment_func.sce
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// BM4321 Genomic Signal Processing
//
// Standalone function file for alignment
//
// Operations
// 1. Global Search
// 2. Local Search
// 3. Semi-Global Search
//
// Objectives
// 1. Familiarization with basic sequence alignment algorithms
//
// Upeka Premaratne, ENTC, University of Moratuwa ([email protected]) 2016/12/05
// Free to use, distribute and modify for educational purposes with attribution
function g=gap_penalty(k)
// Gap penalty function
g_alpha = 0;
g_beta = 2;
g = -(g_alpha+g_beta*k);
endfunction
function result=prom_base(base_x,base_y,score_m,score_mm)
// Match mismatch score
// score_m - match score
// score_mm - mismatch score
if ((base_x==base_y)|(base_x == ascii('A') & base_y == ascii('W'))|(base_x == ascii('T') & base_y == ascii('W'))) then
result = score_m;
else
result = score_mm;
end
endfunction
function result=comp_base(base_x,base_y,score_m,score_mm)
// Match mismatch score
// score_m - match score
// score_mm - mismatch score
if ((base_x==base_y)|(base_x == ascii('A') & base_y == ascii('W'))|(base_x == ascii('T') & base_y == ascii('W'))) then
result = score_m;
else
result = score_mm;
end
endfunction
function matrix_result = scorematrix_global(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Function to perform global search
len_x = length(seq_x);
len_y = length(seq_y);
basic_mat = zeros(len_x+1,len_y+1);
//Initialize with gap penalties
for k_x=1:(len_x+1)
basic_mat(k_x,1)=gap_penalty(k_x-1);
end
for k_y=1:(len_y+1)
basic_mat(1,k_y)=gap_penalty(k_y-1);
end
//Recurrance relation
for k_x=2:(len_x+1)
for k_y=2:(len_y+1)
score_match = basic_mat(k_x-1,k_y-1)+comp_base(seq_x(k_x-1),seq_y(k_y-1),score_m,score_mm);
score_gap_x = basic_mat(k_x,k_y-1)+gap_penalty(1);
score_gap_y = basic_mat(k_x-1,k_y)+gap_penalty(1);
basic_mat(k_x,k_y)=max([score_match score_gap_x score_gap_y]);
end
end
matrix_result = basic_mat;
endfunction
function [align_x,align_y] = traceback_global(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Traceback for global alignment
score_matrix = scorematrix_global(seq_x,seq_y,score_m,score_mm,gap_penalty);
len_x = length(seq_x);
len_y = length(seq_y);
base_x = seq_x;
base_y = seq_y;
out_x = [];
out_y = [];
k_x = len_x;
k_y = len_y;
// Perform the traceback
while (k_x>0&k_y>0) then
k_gx = score_matrix(k_x,k_y+1);
k_gy = score_matrix(k_x+1,k_y);
k_diag = score_matrix(k_x,k_y);
k_c = score_matrix(k_x+1,k_y+1);
if k_c==k_diag+comp_base(seq_x(k_x),seq_y(k_y),score_m,score_mm) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,base_y(k_y)];
k_x=k_x-1;
k_y=k_y-1;
elseif k_c==k_gx+gap_penalty(1) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,45];
k_x=k_x-1;
elseif k_c==k_gy+gap_penalty(1) then
out_x = [out_x,45];
out_y = [out_y,base_y(k_y)];
k_y=k_y-1;
end
end
// Write the output
if (k_x>0&k_y==0) then
pre_x = ascii(base_x(1:k_x));
pre_y = ascii(45*ones(1,k_x));
align_x = strcat([pre_x,strrev(ascii(out_x))]);
align_y = strcat([pre_y,strrev(ascii(out_y))]);
elseif (k_x==0&k_y>0) then
pre_y = ascii(base_y(1:k_y));
pre_x = ascii(45*ones(1,k_y));
align_x = strcat([pre_x,strrev(ascii(out_x))]);
align_y = strcat([pre_y,strrev(ascii(out_y))]);
else
align_x = strrev(ascii(out_x));
align_y = strrev(ascii(out_y));
end
endfunction
function matrix_result = scorematrix_local(seq_x,seq_y,score_m,score_mm,gap_penalty)
//Function to perform local search
len_x = length(seq_x);
len_y = length(seq_y);
basic_mat = zeros(len_x+1,len_y+1);
//No need to initialize because gap penalty will always be negative
//Recurrance relation
for k_x=2:(len_x+1)
for k_y=2:(len_y+1)
score_match = basic_mat(k_x-1,k_y-1)+comp_base(seq_x(k_x-1),seq_y(k_y-1),score_m,score_mm);
score_gap_x = basic_mat(k_x,k_y-1)+gap_penalty(1);
score_gap_y = basic_mat(k_x-1,k_y)+gap_penalty(1);
basic_mat(k_x,k_y)=max([score_match score_gap_x score_gap_y 0]); // Add the zero to global search
end
end
matrix_result = basic_mat;
endfunction
function [align_x,align_y,n] = traceback_local(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Traceback for local alignment
score_matrix = scorematrix_local(seq_x,seq_y,score_m,score_mm,gap_penalty);
//disp(score_matrix');
len_x = length(seq_x);
len_y = length(seq_y);
base_x = seq_x;
base_y = seq_y;
out_x = [];
out_y = [];
[m,n]=max(score_matrix); // m - is maximumm value with smallest indices / n - indices [x,y]
//disp(m);
//disp(n);
k_x = n(1,1)-1;
k_y = n(1,2)-1;
//disp(k_x);
//disp(k_y);
post_x = ascii(seq_x((k_x+1):len_x));
post_y = ascii(seq_y((k_y+1):len_y));
// Perform the traceback
while (k_x>0&k_y>0) then
k_gx = score_matrix(k_x,k_y+1);
k_gy = score_matrix(k_x+1,k_y);
k_diag = score_matrix(k_x,k_y);
k_c = score_matrix(k_x+1,k_y+1);
if k_c==k_diag+comp_base(seq_x(k_x),seq_y(k_y),score_m,score_mm) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,base_y(k_y)];
k_x=k_x-1;
k_y=k_y-1;
elseif k_c==k_gx+gap_penalty(1) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,45];
k_x=k_x-1;
elseif k_c==k_gy+gap_penalty(1) then
out_x = [out_x,45];
out_y = [out_y,base_y(k_y)];
k_y=k_y-1;
elseif k_c==0;
break;
end
end
// Write the output
if (k_x>0&k_y==0) then
pre_x = ascii(base_x(1:k_x));
pre_y = ascii(45*ones(1,k_x));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
elseif (k_x==0&k_y>0) then
pre_y = ascii(base_y(1:k_y));
pre_x = ascii(45*ones(1,k_y));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
else
align_x = strrev(ascii(out_x));
align_y = strrev(ascii(out_y));
end
n =[k_x+1,k_y+1];
endfunction
function matrix_result = scorematrix_prom(seq_x,seq_y,score_m,score_mm,gap_penalty)
//Function to perform local search
len_x = length(seq_x);
len_y = length(seq_y);
basic_mat = zeros(len_x+1,len_y+1);
//No need to initialize because gap penalty will always be negative
//Recurrance relation
for k_x=2:(len_x+1)
for k_y=2:(len_y+1)
score_match = basic_mat(k_x-1,k_y-1)+prom_base(seq_x(k_x-1),seq_y(k_y-1),score_m,score_mm);
score_gap_x = basic_mat(k_x,k_y-1)+gap_penalty(1);
score_gap_y = basic_mat(k_x-1,k_y)+gap_penalty(1);
basic_mat(k_x,k_y)=max([score_match score_gap_x score_gap_y 0]); // Add the zero to global search
end
end
matrix_result = basic_mat;
endfunction
function [align_x,align_y] = traceback_prom(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Traceback for local alignment
score_matrix = scorematrix_prom(seq_x,seq_y,score_m,score_mm,gap_penalty);
//disp(score_matrix');
len_x = length(seq_x);
len_y = length(seq_y);
base_x = seq_x;
base_y = seq_y;
out_x = [];
out_y = [];
[m,n]=max(score_matrix);
k_x = n(1,1)-1;
k_y = n(1,2)-1;
post_x = ascii(seq_x((k_x+1):len_x));
post_y = ascii(seq_y((k_y+1):len_y));
// Perform the traceback
while (k_x>0&k_y>0) then
k_gx = score_matrix(k_x,k_y+1);
k_gy = score_matrix(k_x+1,k_y);
k_diag = score_matrix(k_x,k_y);
k_c = score_matrix(k_x+1,k_y+1);
if k_c==k_diag+prom_base(seq_x(k_x),seq_y(k_y),score_m,score_mm) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,base_y(k_y)];
k_x=k_x-1;
k_y=k_y-1;
elseif k_c==k_gx+gap_penalty(1) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,45];
k_x=k_x-1;
elseif k_c==k_gy+gap_penalty(1) then
out_x = [out_x,45];
out_y = [out_y,base_y(k_y)];
k_y=k_y-1;
elseif k_c==0;
break;
end
end
// Write the output
if (k_x>0&k_y==0) then
pre_x = ascii(base_x(1:k_x));
pre_y = ascii(45*ones(1,k_x));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
elseif (k_x==0&k_y>0) then
pre_y = ascii(base_y(1:k_y));
pre_x = ascii(45*ones(1,k_y));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
else
align_x = strrev(ascii(out_x));
align_y = strrev(ascii(out_y));
end
endfunction
function matrix_result = scorematrix_semiglobal(seq_x,seq_y,score_m,score_mm,gap_penalty)
//Function to perform local search
len_x = length(seq_x);
len_y = length(seq_y);
basic_mat = zeros(len_x+1,len_y+1);
//No need to initialize because gap penalty will always be negative
//Recurrance relation
for k_x=2:(len_x+1)
for k_y=2:(len_y+1)
score_match = basic_mat(k_x-1,k_y-1)+comp_base(seq_x(k_x-1),seq_y(k_y-1),score_m,score_mm);
score_gap_x = basic_mat(k_x,k_y-1)+gap_penalty(1);
score_gap_y = basic_mat(k_x-1,k_y)+gap_penalty(1);
basic_mat(k_x,k_y)=max([score_match score_gap_x score_gap_y]); // Same as global search
end
end
matrix_result = basic_mat;
endfunction
function [align_x,align_y] = traceback_semiglobal(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Traceback for semi-global alignment
// Assuming x is longer than y to make code simpler
score_matrix = scorematrix_semiglobal(seq_x,seq_y,score_m,score_mm,gap_penalty);
len_x = length(seq_x);
len_y = length(seq_y);
base_x = seq_x;
base_y = seq_y;
out_x = [];
out_y = [];
k_x = len_x;
[n_max,k_y] = max(score_matrix(len_x+1,:));
k_y=k_y-1;
post_x = ascii(seq_x((k_x+1):len_x));
post_y = ascii(seq_y((k_y+1):len_y));
// Perform the traceback
while (k_x>0&k_y>0) then
k_gx = score_matrix(k_x,k_y+1);
k_gy = score_matrix(k_x+1,k_y);
k_diag = score_matrix(k_x,k_y);
k_c = score_matrix(k_x+1,k_y+1);
if k_c==k_diag+comp_base(seq_x(k_x),seq_y(k_y),score_m,score_mm) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,base_y(k_y)];
k_x=k_x-1;
k_y=k_y-1;
elseif k_c==k_gx+gap_penalty(1) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,45];
k_x=k_x-1;
elseif k_c==k_gy+gap_penalty(1) then
out_x = [out_x,45];
out_y = [out_y,base_y(k_y)];
k_y=k_y-1;
end
end
// Write the output
if (k_x>0&k_y==0) then
pre_x = ascii(base_x(1:k_x));
pre_y = ascii(45*ones(1,k_x));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
elseif (k_x==0&k_y>0) then
pre_y = ascii(base_y(1:k_y));
pre_x = ascii(45*ones(1,k_y));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
else
align_x = strrev(ascii(out_x));
align_y = strrev(ascii(out_y));
end
endfunction
//New modified function
function [align_x,align_y,n] = traceback_prom_modified(seq_x,seq_y,score_m,score_mm,gap_penalty)
// Traceback for local alignment
score_matrix = scorematrix_prom(seq_x,seq_y,score_m,score_mm,gap_penalty);
//disp(score_matrix');
len_x = length(seq_x);
len_y = length(seq_y);
base_x = seq_x;
base_y = seq_y;
out_x = [];
out_y = [];
[m,n]=max(score_matrix);
k_x = n(1,1)-1;
k_y = n(1,2)-1;
post_x = ascii(seq_x((k_x+1):len_x));
post_y = ascii(seq_y((k_y+1):len_y));
// Perform the traceback
while (k_x>0&k_y>0) then
k_gx = score_matrix(k_x,k_y+1);
k_gy = score_matrix(k_x+1,k_y);
k_diag = score_matrix(k_x,k_y);
k_c = score_matrix(k_x+1,k_y+1);
if k_c==k_diag+prom_base(seq_x(k_x),seq_y(k_y),score_m,score_mm) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,base_y(k_y)];
k_x=k_x-1;
k_y=k_y-1;
elseif k_c==k_gx+gap_penalty(1) then
out_x = [out_x,base_x(k_x)];
out_y = [out_y,45];
k_x=k_x-1;
elseif k_c==k_gy+gap_penalty(1) then
out_x = [out_x,45];
out_y = [out_y,base_y(k_y)];
k_y=k_y-1;
elseif k_c==0;
break;
end
end
// Write the output
if (k_x>0&k_y==0) then
pre_x = ascii(base_x(1:k_x));
pre_y = ascii(45*ones(1,k_x));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
elseif (k_x==0&k_y>0) then
pre_y = ascii(base_y(1:k_y));
pre_x = ascii(45*ones(1,k_y));
align_x = strcat([pre_x,strrev(ascii(out_x)),post_x]);
align_y = strcat([pre_y,strrev(ascii(out_y)),post_y]);
else
align_x = strrev(ascii(out_x));
align_y = strrev(ascii(out_y));
end
endfunction