#! 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