long running time

hi,

i have code (smith_waterman) algorithm of sequence alignment.

I have to align one sequence to large set of squences (database) when run it, it take very long time .

can any one reduce the running time by reducing steps?

Note: I do not know why be the running time longer when used large database. i.e when I align one sequence to 100 sequences from array with size(7000*1000) for example the time will be longer when align one sequence to 100 sequences from array with size(200*1000)

this is code:

f1=fopen('d:\matlab11\r2011a\bin\webscopdata\webscop\action.txt');

c=textscan(f1,'%d%d');fclose(f1);c1=double(c{1});c2={2};
[p,o]=hist(c1,unique(c1));celcod=dlmread('d:\matlab11\r2011a\bin\webscopdata\webscop\webfinal.txt');

gap = -1;

for b=1

      f=0;cc=1;

      for b1=1:10

          if b~=b1

match=2;mismatch=-1;align1=[];align2=[];x=celcod(b,:);   y=celcod(b1,:);

x1(1:length(y),1:length(x))=0; trac(1:length(y),1:length(x))=0;

txt(1:length(y),1:length(x))=' ';       mat=struct('scor',x1,'pointer',txt);

                  for j=1:length(x)

     mat(1,j).scor=x1(1,j);     mat(1,j).pointer='none';
                  end

                  for i=1:length(y)

     mat(i,1).scor=x1(i,1);   mat(i,1).pointer='none';
                  end

max_i=1;max_j=1;max_scor=1;score=0;

                   for i=2:length(y)

                       for j=2:length(x)

                 letter1=x(j);letter2=y(i);

                           if strcmp(letter1,letter2)

                              dig_scor=mat(i-1,j-1).scor+match;

                           else

                              dig_scor=mat(i-1,j-1).scor+mismatch; 

                           end

   up_scor=mat(i-1,j).scor+gap;  eft_scor=mat(i,j-1).scor+gap;

        if (dig_scor<=0 && up_scor<=0 && left_scor<=0)
         mat(i,j).scor = 0;   mat(i,j).pointer='none';
                                continue

                           end

                          if dig_scor>=up_scor

                                  if dig_scor>=left_scor

    mat(i,j).scor=dig_scor; mat(i,j).pointer='diagonal';

                                       else

   mat(i,j).scor=left_scor; mat(i,j).pointer='left';

                                  end

                          else

                                  if up_scor>=left_scor
     mat(i,j).scor=up_scor;  mat(i,j).pointer='up';

                                  else

     mat(i,j).scor=left_scor;  mat(i,j).pointer='left';

                                  end

                          end

                          if mat(i,j).scor > max_scor

        max_i=i;  max_j=j; max_scor=mat(i,j).scor;

                          end;end;end

               max_scor;j=max_j; i=max_i;

       while i>1 & j>1

                  if strcmp(mat(i,j).pointer,'none')==1

                     break;  end

                 if strcmp(mat(i,j).scor,'0')==1

                     break;

                  end

                 if strcmp(mat(i,j).pointer,'diagonal')==1

    align1= [align1 x(j)];align2=[align2 y(i)]; trac(i,j)=1;

                      if strcmp(x(j),y(i))==1

                          score=score+2;

                      else

                          score=score-1;  end

                  i=i-1; j=j-1;

                  elseif strcmp(mat(i,j).pointer,'left')==1;

     align1= [align1 x(j)];align2=[align2 '-'];

                trac(i,j)=1;j=j-1;score=score-1;

                 else mat(i,j).pointer=='up'

   align1= [align1 '-' ]; align2=[align2 y(i)];trac(i,j)=1;

                          i=i-1; score=score-1;

                  end; end

                align1=fliplr(align1);align2=fliplr(align2);

                 [align1;align2];

                  for i=1:length(y)

                      for j=1:length(x)

        mat1(i,j)=mat(i,j).scor;  mat2{i,j}=mat(i,j).pointer;

                      end

                  end

                scor(b1)=max_scor; 

                        end

       end

end

thanks in advance