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]

I think that's an excellent idea, especially given the general consistency of the format (only 210 is inconsistent in that it doesn't use a :, and then 400 is redundant in that it lists the seq id first). Here's my whack:
Read more... (11 kB)

MJD says "you can't just make shit up and expect the computer to know what you mean, retardo!"

I run a Win32 PPM repository for perl 5.6.x and 5.8.x -- I take requests (README).

** The third rule of perl club is a statement of fact: pod is sexy.

Unless I miss something obvious, the language you're parsing is regular. Parse::RecDescent is a tool to deal with context free languages. Since every regular language is context free, you can use Parse::RecDescent to deal with it, but it's overkill.

Parsing a context free language is a relatively costly process compared to parsing a regular language (O(n^3) vs. O(n)) and since you're parsing lots of data, that is quite a difference. In this case it would almost certainly be much faster to implement your own parser as was suggested above.

Just my 2 cents, -gjb-

Yeah, Parse::RecDescent is really slow. If you really want to use a parse module, then you can have a look at Parse::YAPP. (See "Re:x2 Easy Things (a plug for Parse::YAPP)" for grinder's opinion.)

Now, as to your grammar, did you really mean to hardcode the linenumber in seq_count    : "<160> NUMBER OF SEQ ID NOS:" /\d+/? Are you sure you didn't want seq_count    : "<" /\d+/ "> NUMBER OF SEQ ID NOS:" /\d+/?
update: Take a look at OPTIMIZING YOUR GRAMMARS in Parse::RecDescent::FAQ.

I'm pretty sure that this format is something the PSIPS people just made up and that BP doesn't have anything for it (not that their stuff is exactly speedy, either).

Thanks for all the help though.