Hi Khen1950fx, thank you for your help. I have copyed you code, and run on my computer(just change the path of the file). However I get the same error message, "the sequence does not to be FASTA format(lacks a descriptor line '>')". The code I run as following:

#!/localperl/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new(
          -file   =>  "/home/zhaoy/document/perl/lwp/seq.fasta",
          -format => 'FASTA');
my $out = Bio::SeqIO->new(
          -file   => ">/home/zhaoy/document/perl/lwp/new_out.log",
          -format => "EMBL" );
while ( my $seq = $in->next_seq() ) {
        print $out->write_seq($seq), "\n";
}
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I receive the error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The sequence does not appear to be FASTA format (lacks a descript
+or line '>')
STACK: Error::throw
STACK: Bio::Root::Root::throw /localperl/lib/site_perl/5.12.4/Bio/Root
+/Root.pm:368
STACK: Bio::SeqIO::fasta::next_seq /localperl/lib/site_perl/5.12.4/Bio
+/SeqIO/fasta.pm:127
STACK: tmhmm.pl:12
-----------------------------------------------------------
[download]

The same program, gain different results. Maybe the problem is that the installation of bioperl. But I am not sure.