I'm not sure what you are trying to do, but there are a number of obvious errors in your code.

  1. $element=$_; most likely sets $element to undef - $_ does not contain whatever you think it does
  2. $element used in foreach $element is not the same $element used in print " $h{$element}";. The value used with the hash is most likely undef.
  3. $h{$element}=$domains1[$i+1]; replaces the value from the $h{$element}=$domains1[$i-1]; assignment.

If resolving the errors pointed out above doesn't fix your problem then you should show us a small sample of your input data and the output you expect from it. Maybe though you want to achieve something like:

use strict;
use warnings;

my $list = <<LIST;
PF10417.3
PF11001.3
PF05.3
LIST

my @domains1 = ('PF05.3',     'PF11001.3', 'PF00389.24', 'PF10417.3');
my @domains2 = ('PF01',       'PF02',      'PF11001.3',  'PF00389');
my @domains3 = ('PF00389.24', 'PF05.3',    'PF01',       'PF00389');
my %neighbours;

for my $domain (\@domains1, \@domains2, \@domains3) {
    for my $idx (0 .. $#$domain) {
        my @near = grep {$_ >= 0 && $_ <= $#$domain} $idx - 1, $idx + 
+1;
        push @{$neighbours{$domain->[$idx]}}, map {$domain->[$_]} @nea
+r;
    }
}

open my $inList, '<', \$list or die "cannot open 'domainlist'becuase:$
+!";

while (defined (my $domain = <$inList>)) {
    chomp $domain;

    print "Domain $domain has neighbours: @{$neighbours{$domain}}\n";
}

[download]

Prints:

Domain PF10417.3 has neighbours: PF00389.24
Domain PF11001.3 has neighbours: PF05.3 PF00389.24 PF02 PF00389
Domain PF05.3 has neighbours: PF11001.3 PF00389.24 PF01

[download]
True laziness is hard work

In reply to Re: finding neighbors of an element in arrays by GrandFather
in thread finding neighbors of an element in arrays by persianswallow

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