it would be great to have support for -d and -u as implemented for blastcl3
-d Database [String] default = nr
-u Restrict search of database to results of Entrez2 lookup [String] Optional
with -d you you can choose databases besides nt - like EST databases - who could live without?
with -u you can limit search by organism which is nice (you could provide list of organisms to choose from)
also you can limit to refseq only, which is VERY HANDY