Hi Mokers, Please help me with the 'out of memory' issue. My input file <PROTEOME> is around 30mb (due to which i assume my program is not running as expected), please advice me regarding improvement of the script and avoid populating unwanted memory. Below is my code for your ref. Thanks

#!/usr/bin/perl
use 5.010;
use strict;
use warnings;
use diagnostics;
open GENES,'genes.txt' or print "cant open genes\t";
open LOG,'log.txt' or print "cant open log\t";
open START,'start.txt' or print "cant open start\t";
open STOP,'stop.txt' or print "cant open stop\t";
open DIST,'diff.txt' or print "cant open diff";
open O,'>logratio_g0_revised_withnp.txt';
my @genes=<GENES>;
my @start=<START>;
my @stop=<STOP>;
my @log=<LOG>;
my @dist=<DIST>;
chomp @genes;
chomp @start;
chomp @stop;
chomp @log;
chomp @dist;
my $index=0;
my $index1=1;
my $ind=0;
my $in=0;
my $count=1;
do
{
    $ind=0;
    $ind1=1;
    $hit=0;
    undef @hold;
    undef @aminoacid;
    if($proteome[$index]=~m/^>/)
    {
        $val++;
        $proteome[$index] =~ /\|(.+)\|(.+)$/;
        $id=$1;
        $name=$2;
        $index++;
        print O "$name\t$id\t";
        push @hold,$proteome[$index];
        $index++;
        do
        {
            push @hold,$proteome[$index];
            $index++;
        }
        until($proteome[$index]=~m/^>/);
        $peptide= join ('', @hold);
        undef @hold;
        @aminoacid=split(//,$peptide);    
    }
        if(@aminoacid>0)
        {
        do
        {
            if($aminoacid[$ind]=~/^X$/)
            {
                $ind++;
                $ind1++;
            }
            else
            {
            if($aminoacid[$ind] eq $aminoacid[$ind1])
            {
                
                do
                {
                    $hit++;
                    $ind++;
                    $ind1++;
                    
                }
                until($aminoacid[$ind] ne $aminoacid[$ind1] or $ind==@
+aminoacid);
                $hit++;
                if($hit>9)
                {
                    print O "$aminoacid[$ind]\t$hit\t";    
                }
                else
                {
                    $hit=0;
                }
                $ind++;
                $ind1++;
                $hit=0;
            }
            else
            {
                $ind++;
                $ind1++;
            }
            }
            
            
        }
        until($ind==@aminoacid);
        undef @aminoacid;
        print O "\n";
    }        
}
until($index==@proteome);
say $val;
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