Hi,

I have a following problem which try to score the substrings distance.
The score is basically the number of positions of substrings that occur (dotted count)

And these are the three instances:
Instance 1 (score 21) 
.......    .......   ......
GATTACGAGTGGCGCTCGTGTAACGGCA
GATTACG    GCGCTCG   AACGGCA

[download]
Instance 2 (score 16) 
.........       .......
GATTACGAGTGGCGCTCGTGTAACGGCA
GATTACG
  TTACGAG       CGTGTAA

[download]
Instance 3 (score 17) 
             GCTCGTG
  ..................
GATTACGAGTGGCGCTCGTGTAACGGCA
   TACGAGT
        GTGGCGC

[download]
UPDATE: Instance 4 (score 4) 
          ..            ..     
GATTACGAGTGGCGCTCGTGTAACGGCA
          GG            GG

[download]
I wonder if there is a way to solve this.
Currently, what I have is: 
#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my $s1 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';

# Here are the array of the substrings, note that the number of 
# substrings may differ from array to array
# and length of the substring may vary (defined as a parameter) 

my @ar  =  ('GATTACG','GCGCTCG','AACGGCA');  #21 (0,11,21)
my @ar2 =  ('GATTACG','TTACGAG','CGTGTAA');  #16
my @ar3 =  ('TACGAGT','GTGGCGC','GCTCGTG');  #17
my @ar4 =  ('GG','GG');                      #4


score($s1,\@ar2);

sub score{
  my ($str,$array) = @_;
  my @pos;
  my $sub_len = length @$array[1];

  foreach (@$array){
        my $idx = index $s1, $_;
        push @pos, $idx;
        print "$idx\n";
      }

     # I'm not sure where to go from here
     for (0..$#pos){
         my $sum = $pos[$_]+$sub_len;
           
        }

   }

[download]
UPDATE 2: Renamed title.
Regards,
Edward

In reply to Measuring Substrings Problem by monkfan

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