my $stringfh = new IO::String($sequence_string); my $seqio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta'); my $blaster = Bio::Tools::Run::StandAloneBlast->new(@params); #### while( my $seq = $seqio->next_seq ) { my $blast_report = $blaster->blastall($seq); ... while( my $BLAST_result = $blast_report->next_result ) { ... while( my $hit = $BLAST_result->next_hit ) { ... } } }