I didn't get any problem when I ran it this way:

#!/usr/bin/perl -w
                                                                      
+          
# Strict (always using these 2 lines will save you much grief!)
use strict;
use warnings;
                                                                      
+          
# Global variables
my @next_cell_arr;
my @protein_matrix;
my @sequence_1_arr;
my @sequence_2_arr;
my $row = 0;
my $col = 0;
my $dowhat = 0;
                                                                      
+          
# Generate some test data
$protein_matrix[$row][$col]     = 1;
$protein_matrix[$row][$col+1]   = 2;
$protein_matrix[$row+1][$col]   = 3;
$protein_matrix[$row+1][$col+1] = 4;
                                                                      
+          
# BioBoy's code follows
push( @next_cell_arr, $protein_matrix[$row][$col+1] );
push( @next_cell_arr, $protein_matrix[$row+1][$col+1] );
push( @next_cell_arr, $protein_matrix[$row+1][$col] );
                                                                      
+          
# - debug
#$arr_len = scalar @next_cell_arr;
#for( $var = 0; $var < $arr_len; $var++ ){
#    print $next_cell_arr[$var];
#    print "\n";
#}
#print "\n\n";
#exit;
# - debug
                                                                      
+          
# - if all values are equal, then the sequence gets a match of suffers
+ a mismatch
# (diagonal move), and not a gap penalty.  This also saves me from hav
+ing to
# compute the max of the three cells
if( ($next_cell_arr[0] == $next_cell_arr[1]) && ($next_cell_arr[1] == 
+$next_cell_arr[2]) ){
        push( @sequence_2_arr, $protein_matrix[0][$col+1] );
        push( @sequence_1_arr, $protein_matrix[$row+1][0] );
        $dowhat = "diagonal";
}
[download]

But if you're getting an error on such-and-such a line, I'd like to suggest you try putting debugging right near that line, and breaking it up into multiple statements, so you can see the intermediate values of interest:

#TFD (Temporary for debug)>>
my $cell0 = $next_cell_arr[0] || die "cell0 undef!\n"; printf "Cell0 =
+ %s\n", $cell0;
my $cell1 = $next_cell_arr[1] || die "cell1 undef!\n"; printf "Cell1 =
+ %s\n", $cell1;
my $cell2 = $next_cell_arr[2] || die "cell2 undef!\n"; printf "Cell2 =
+ %s\n", $cell2;

if( ($cell0 == $cell1) && ($cell1 == $cell2) ){
        print "TFD> All 3 cell values defined and EQUAL\n";
        push( @sequence_2_arr, $protein_matrix[0][$col+1] );
        push( @sequence_1_arr, $protein_matrix[$row+1][0] );
        $dowhat = "diagonal";
}
print "TFD> All 3 cell values defined, but NOT equal\n";
[download]

(Note that I use the notation "TFD" to mean that a line or a sequence of lines is "temporary for debugging", and can be removed once I uncovered the cause of the problem).

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