use Bio::SeqIO;

my $filename = 'test.seq';
my $format = 'fasta';

my $seqio = Bio::SeqIO->new( -file => $filename, -format => $format );
while ( my $seqobj = $seqio->next_seq() ) {
   my $raw_sequence = $seqobj->seq;
   # do your searching on this raw sequence
}