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
   }