open( FASTAFILE, $ARGV[0] );
while (<FASTAFILE>) {

    if ( /^>/ && $seqflag == 1 ) {
        push ( @sequences, $fasta );
        $fasta = "";
        $fasta = $_;

    }
    elsif (/^>/) {

        $fasta   = $_;
        $seqflag = 1;

    }
    else {

        $fasta .= $_;

    }
}

push ( @sequences, $fasta );
#then iterate @sequences to run over BLAST