There could be one additional reason why running Blast with the flag "-a 2" on a dual-processor SMP could be of advantage: it needs less memory than two (independent) Blast jobs simultaneously running on the same node. Can somebody tell me the simplest (or most elegant) way of submitting "blast -a 2" jobs through SGE? Ivo P.S. Perhaps: qsub -pe threads 2 <my_blast_script>? Or something else instead of threads?