Adrade,
Thanks so much for your reply. I've included your part in my code. Somehow your approach doesn't consider the maximum span *in the given query*.
For example with query: "ACD" it gives 
S4 ABIC
S1 AB-C
S2 A--C

[download]
i.e it left out the "D" for alignment (kindly see answers above). In other case, given query "AB" it over-aligned them, it gives: 
S4 ABICID
S2 A--C-D
S1 AB-C-D

[download]
Is there any way I can go about it in your code. Hope to hear from you again.

Update: Finally! with some tweak suggested by Adrade below. I can get the problem SOLVED! Many thanks for the rest of you, especially Adrade. Don't know what to say! For those who are interested in the final form of the code, check this out:
# With major improvement by "canonizable" Adrade :-)

sub align_v3
{
    my ($hashref,$seq) = @_;
    my @in = split(/\s/,$seq);
    my $test = join('(.*?)',@in);
    
    my @hyph_padded_seq;
    my @sequences;

   my $reduce;
   for (keys %$hashref) { $reduce = length(${$hashref->{$_}}[0]); 
   last; }

    for my $key( sort {$a cmp $b} keys(%$hashref))
    {

        my $string = join('',@{$hashref->{$key}});
       
        if($string =~ $test)
        {
           push(@sequences, $hashref->{$key});
        }

    }

    my $regex = '.*'.join('(.*)',@in).'.*';
    my @in_the_running;
    my $biglen = 0;

    for (@sequences) 
    {
        my @letters = @$_; # split(//,$_);

        s/.*($in[0].*$in[$#in]).*/$1/;

        my ($first, $last) = (0,0);
        for (@letters) { last if $_ eq $in[0]; $first++; }
        for (reverse @letters) { last if $_ eq $in[$#in];
        $last++; 
       }
        $last = $#letters - $last;

        @letters = @letters[$first..$last];
        my $asstr = join('',@letters);


        if ((my @gaps) = ($asstr =~ m/$regex/o))
        {
            my $len = length(join('',@gaps)) / $reduce;
            if ($len > $biglen) 
            { 
                unshift(@in_the_running, [ @letters ]); 
                $biglen = length(join('',@gaps)); 

            }
            elsif ($len == $biglen)
            {
                unshift(@in_the_running, [ @letters ]);

            }
            else 
            { 
                push(@in_the_running, [ @letters ]);
            }
        }
    }


    #print @{$in_the_running[0]}, "\n";
    push @hyph_padded_seq, join('',@{$in_the_running[0]}); 

    my @base = @{$in_the_running[0]};

    for my $seqno (1..$#in_the_running) 
    {
        # my @seq = split(//,$in_the_running[$seqno]);
        my @seq = @{$in_the_running[$seqno]};
        my $count = $#base;
        my @disp;

        for my $q (reverse @base) 
        {

          if (($seq[$#seq] eq $q) || ($count == $#seq))
          {
              push(@disp, pop(@seq));
          }
          else 
          { 
              push(@disp, '-' x $reduce);
          }
          $count--;
        }
        push @hyph_padded_seq, join('', reverse(@disp));
        #print reverse(@disp), "\n";
   }
     
    return @hyph_padded_seq; 
}

# A hash version can be found here: http://paste.phpfi.com/61624

[download]
Regards,
Edward

In reply to Re^2: Simple String Alignment by monkfan
in thread Simple String Alignment by monkfan

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