use Bio::FASTASequence; my $fasta = ">sp|P01815|HV2B_HUMAN Ig heavy chain V-II region COR - Homo sapiens (Human). QVTLRESGPALVKPTQTLTLTCTFSGFSLSSTGMCVGWIRQPPGKGLEWLARIDWDDDKY YNTSLETRLTISKDTSRNQVVLTMDPVDTATYYCARITVIPAPAGYMDVWGRGTPVTVSS "; my $object = Bio:FASTASequence->new( $fasta ); my $sequence = $object->getSequence;