I'm the guy who started this thread, and I wanted to follow up with some code that I wrote, and ask other monks if this is ok. Again, thanks in advance.

sub blast
{
    my $data = shift;
    my $temp = "$ENV{HOME}/temp/seq.tmp";
    my $fifo = "ssh myhost /path/to/blast";
    my @args = ('-p blastn', '-d nt', '-e 0.0000001', '-m 7');
    
    ### load input file with fasta-formatted queryid/sequence ###
    open  SEQ, ">$temp" or die "Could not open for write:$!";
    print SEQ  ">",$data->[0],"\n",$data->[1];    
    close SEQ;

    ### open a handle to BLAST output, retry if unsuccessfull ###
    {
        if (!open BLAST, "$fifo @args <$temp|")
        {
            #
            print LOG "BLAST connection refused, retrying...\n";
            #
            sleep(300);
            redo;
        }
    }

    ### process the report ###
    parse(*BLAST);
}
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