gistfile1.txt

#!/usr/bin/perl -w

use strict;

# Filenames
my $start10 = 'start10.dat';
my $res10 = 'res10.dat';

# Opening the files
open (START, '<', $start10) or die "Could not read file\n";
open (RES, '<', $res10) or die "Could not read file\n";

# Creating a hash with all start entries
my %start_list = ();
while (defined (my $line = <START>)) {
   chomp $line;
   $start_list{$line} = undef;
}

# Creating an array with all accession numbers in the result file
my %res_list = ();
while (defined (my $line = <RES>)) {
   chomp $line;
   $res_list{$1} = undef if $line =~ m/\b(\w+.CDS.1)\b/;
}

# Printing a list of accsseion numbers not detected in the result file
print "Following list cotains accession numbers present in '$start10' but not in '$res10'\n";
foreach my $entry (keys %start_list) {
   if (!exists $res_list{$entry}) {
      print "$entry\n";
   }
}