@newrecord = ();
   # Send the record to have any blank lines removed.
   @newrecord = CleanData( $record );

   -vs- 
   $newrecord = CleanData( $record );
   
    sub CleanData {
       my( $record ) = $_[0];
       my ($cleanrecord, $line );
   
       ### Separate the record by newlines.
       @$record = split /\n/, $record;

       ### Remove empty lines if they exist.
       foreach ( @$record ) {
         chomp;
         next if /^\s+$/;
         push @$cleanrecord, $_;
     }
     $cleanrecord;
  }

##</code><code>##

 if ($line =~ m/CHROMOSOME:\s*(\d*)\s*$/)
    {
      $chrome_num = $1;
    }

    # Get TIGR model's reference id
    if ($line =~ m/MODEL_NAME:\s*(.*)$/)
    {
      $tigr_id = $1;
    }

    # Get the locus on the bac where the gene was cloned.
    if ($line =~ m/BAC_LOCUS:\s*(.*)\s*$/)
    {
      $bac_locus = $1;
    }

    ....
  
    might go better as

   if( $line =~ m/(.*?):\s+(\S+)\s+/o ) {
       $type = $1;
       $info = $2;
   }
 
   if( $type eq "CHROMOSONE" ) {
      # do whatever
   } elseif( $type eq "NUM_FOO ) {
      # do num foo
   }