#! perl -slw
use strict;
use Data::Dumper;

local $/ = '>';

my @sequences;

(undef) = scalar <>;

my $start = time;
while( my $record = <> ) {
    my @lines = split "\n", $record;
    pop @lines if $lines[-1] eq '>';
    my $desc  = shift @lines;
    my $seq = join'', @lines;

    print $desc;
}
printf STDERR "Took %d seconds\n", time() - $start;

__END__
c:\test>fasta test.fasta >nul
Took 11 seconds

c:\test>dir test.fasta
27/07/2010  22:40       201,116,583 test.fasta

c:\test>tail test.fasta
CGCGCCTCAGCGGGGGAGGTCCGTATGACCCCGTCCATTGATTCGAACTGCCTAGTCCCCTGGATGACAA
>seq1058200: Some other descriptive text here
CAGGGCGGTTCATTCGCGGACCTATGGCATCCTGGCACTCAACCGGGACTGCGACCAACAATTTTGTCAA
CGCGCCTCAGCGGGGGAGGTCCGTATGACCCCGTCCATTGATTCGAACTGCCTAGTCCCCTGGATGACAA
>seq1058201: Some other descriptive text here
CAGGGCGGTTCATTCGCGGACCTATGGCATCCTGGCACTCAACCGGGACTGCGACCAACAATTTTGTCAA
CGCGCCTCAGCGGGGGAGGTCCGTATGACCCCGTCCATTGATTCGAACTGCCTAGTCCCCTGGATGACAA
>seq1058202: Some other descriptive text here
CAGGGCGGTTCATTCGCGGACCTATGGCATCCTGGCACTCAACCGGGACTGCGACCAACAATTTTGTCAA
CGCGCCTCAGCGGGGGAGGTCCGTATGACCCCGTCCATTGATTCGAACTGCCTAGTCCCCTGGATGACAA

##</code><code>##

c:\test>fasta  \dell\test\fasta\na_clones.dros.RELEASE2.5
BACH50G05 : AC011761, 108350 bases, from X:19.
BACH57F14 : AC018478, 103809 bases, from 4:101.
BACH59K20 : AC010840, 29516 bases, from 4:101.
BACN19N21 : AC010839, 91789 bases, from 4:101.
...
BACR48O22 : AC104149, 193714 bases, from X:01.
BACR48O23 : AC009888, 168719 bases, from 3R:99.
BACR48O24 : AC023722, 191590 bases, from X:01.
BACR48P17 : AC012165, 176195 bases, from X:18.
BACR49A05 : AC008194, 181438 bases, from X:18.
Took 7 seconds