You could do it in two phases:

use 5.006000;  # Perl 5.6.0+

use strict;
use warnings;

use Regexp::List ();

my $txt;

{ # Remove comments.
   open(my $txtfh, '<', $txtf)
      or die("Can't open $txtf : $!\n");

   # Read entire file into memory.
   local $/;
   $txt = <$txtfh>;

   $txt =~ s{/\*.*?\*/}{}sg;  # Remove comments.
   $txt =~ s{/\*.*/}{}s;      # Remve unmatched comment.
}

my @matches = ...;

my $regexp = Regexp::List
             ->new(modifiers => 'i', quotemeta => 0)
             ->list2re(@matches);

open(my $txtfh, '<', \$txt);

while (my $line = <$txtfh>) {
   my @fld = split(/\|/, $line);
   print "$fld[0] $fld[2] sequence=$fld[4] $fld[5]"
      if $line =~ $regexp;
}
[download]

Update: Oops! holli already posted the same thing.