I don't see any obvious problems with your grammar. Indeed, it is very simple, no recursion and little ambiguity. Sometimes P::RD is slower than one would like. But parsing (tens of) gigabytes is a big job in any case. If P::RD is too slow, you might try to roll your own parser: 
while (<DATA>) {
   if (/^<160> NUMBER OF SEQ ID NOS: (\d+)$/) {
      $seq_num = $1;
   }
   elsif (/^<140> CURRENT APPLICATION NUMBER: ([\w\/,]+)$/) {
      $appl_num = $1;
   }
   elsif (/^<210> SEQ ID NO (\d+)$/) {
      $cur_seq = $1;
      $seq{$cur_seq} = {};
   }
   elsif (/^<211> LENGTH: (\d+)$/) {
      $seq{$cur_seq}{length} = $1;
   }
   elsif (/^<212> TYPE: (DNA|PRT)$/) {
      $seq{$cur_seq}{type} = $1;
   }
   elsif (/^<213> ORGANISM: (\w+ \w+)$/) {
      $seq{$cur_seq}{organism} = $1;
   }
   elsif (/^<220> FEATURE:([\w\s]*)$/) {
      $seq{$cur_seq}{feature} = $1;
   }
   elsif (/^<221> NAME\/KEY: (\w+)$/) {
      $seq{$cur_seq}{name_key} = $1;
   }
   elsif (/^<222> LOCATION: ([\d\.\(\)]+)$/) {
      $seq{$cur_seq}{location} = $1;
   }
   elsif (/^<223> OTHER INFORMATION: ([^<]+)$/) {
      $seq{$cur_seq}{other} = $1;
   }
   elsif (/^<400> SEQUENCE: (\d+)$/) {
      $seq{$cur_seq}{seq_num} = $1;
   }
   elsif (/^([\w\s]+)$/) {
      $seq{$cur_seq}{seq} .= $1;
   }
   else {
      die "Unrecognized line: $_\n";
   }
}
foreach my $cur_seq (keys %seq) {
   print "Sequence: $cur_seq,   Organism: $seq{$cur_seq}{organism}\n";
   print "seq: $seq{$cur_seq}{seq}\n\n";
}

__DATA__
<160> NUMBER OF SEQ ID NOS: 727
<140> CURRENT APPLICATION NUMBER: US/09/984,429
<210> SEQ ID NO 1
<211> LENGTH: 733
<212> TYPE: DNA
<213> ORGANISM: Homo sapiens
<400> SEQUENCE: 1
      gggatccgga gcccaaatct tctgacaaaa ctcacacatg cccaccgtgc ccagcacct
+g     60
      aattcgaggg tgcaccgtca gtcttcctct tccccccaaa acccaaggac accctcatg
+a    120
      tctcccggac tcctgaggtc acatgcgtgg tggtggacgt aagccacgaa gaccctgag
+g    180
      tcaagttcaa ctggtacgtg gacggcgtgg aggtgcataa tgccaagaca aagccgcgg
+g    240
      aggagcagta caacagcacg taccgtgtgg tcagcgtcct caccgtcctg caccaggac
+t    300
      ggctgaatgg caaggagtac aagtgcaagg tctccaacaa agccctccca acccccatc
+g    360
      agaaaaccat ctccaaagcc aaagggcagc cccgagaacc acaggtgtac accctgccc
+c    420
      catcccggga tgagctgacc aagaaccagg tcagcctgac ctgcctggtc aaaggcttc
+t    480
      atccaagcga catcgccgtg gagtgggaga gcaatgggca gccggagaac aactacaag
+a    540
      ccacgcctcc cgtgctggac tccgacggct ccttcttcct ctacagcaag ctcaccgtg
+g    600
      acaagagcag gtggcagcag gggaacgtct tctcatgctc cgtgatgcat gaggctctg
+c    660
      acaaccacta cacgcagaag agcctctccc tgtctccggg taaatgagtg cgacggccg
+c    720
      gactctagag gat                                                  
+     733

<210> SEQ ID NO 2
<211> LENGTH: 5
<212> TYPE: PRT
<213> ORGANISM: Homo sapiens
<220> FEATURE:
<221> NAME/KEY: Site
<222> LOCATION: (3)
<223> OTHER INFORMATION: Xaa equals any of the twenty naturally ocurri
+ng L-amino acids
<400> SEQUENCE: 2
      Trp Ser Xaa Trp Ser
        1               5

[download]

-Mark

In reply to Re: Parse::RecDescent help by kvale
in thread Parse::RecDescent help by glwtta

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