You have provided us with your current solution to a problem, but you haven't specified what that problem is. It is difficult to identify what areas might be unneccesary or wasteful in this situation.

Some inline documentation would be useful, as would some additional comments in this thread. Here are a few things that would be nice to know:

• Why is $distance_index and $window random
• More sample data. The $sequence provided is 7 characters, but in this comment you state that it can be over 1000 characters in length. The size of the input data will help determine which algorithm is appropriate.
• How often will this function be called

Hi,
User can send the different values of distance, window and sequence as well. through CGI interface and this refined subroutine will be used inside the package and all the validation controlled by the CGI itself.
. I need to extend my functionality based on this single subroutine , Hence I need to sort it out all the obstacles.My observation is, concerned with Math::Bigint package which created a new object (inside the forloop), I'm using  substr method to pare the characters.
Can you please suggest me, If any where I can improve the performance.
- kulls

For example you could do this (and leave alpha_index as it is):

#!c:\perl\bin\perl
use strict;
use warnings;
use Math::BigInt;
use Data::Dumper;
use Test::More qw(no_plan);
    
    
my %index_val = ( A => 2,
                  C => 3,
                  D => 4,
                  N => 2,
                  M => 2,
                  T => 1,
                  G => 4);

my $sequence       = "ACTGACN";
my $distance_index = 3;
my $window         = 2;

my $arr_ref = alpha_index({ sequence => $sequence,
                           distance => $distance_index,
                           aa_index => \%index_val,
                           window_size => $window });
ok($arr_ref);
diag("Testing alpha_index with window: $window, distance: $distance_in
+dex, sequence: $sequence");
is(ref($arr_ref),'ARRAY','alpha index returned an array');
is(@$arr_ref,7,'7 entries are in the array');
is($arr_ref->[0]{A},2.51025682971601);
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