hi elisheva, thank u so much. my work is done. it took 10 seconds only to process a 300 MB file. i did some changes to modify the program according to the input file. i used a different technique to sort the sequence before seeing your last post.anyways, i still used the sorting the hash part for arranging the headers in the right order :)

#use local so that the setting doesn't interfere with
#other places you might want to read in data.
local $/='>';
open(DATA,"seq.txt") or die "cannot not open";
#load sequences
my %hSequences;
while (my $line = <DATA>) {
  chomp $line;
  next if $line eq '';
  
  #extract data from record
  #  -- s at end of regex needed so that . matches new lines
  my ($subs, $xon, $gid, $sSequences)
    = $line
      =~ /^(\d+)_(\d+)\s+gid(\d+)\s+\d+\s+\d+\s+len=\d+\s+(.*)$/;

  #populate hash
  my $sKey="$gid $subs";
  my $aSequences = $hSequences{$sKey};
  $hSequences{$sKey} = $aSequences = []
    unless defined($aSequences);
  push @$aSequences, split(/\s+/, $xon.$sSequences);
}

my @aKeys = sort(keys(%hSequences));
foreach my $k (@aKeys) {
  my $v = $hSequences{$k};  #get value
  $k =~ s/^/gid/;
  $single=join("", sort @$v);
  $single=~s/[0-9]//g;
  print ">$k\n" . $single . "\n";
}
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