When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working on a bioruby script in which I need to iterate on PSI-BLAST until there are no new sequences added, but I need to use the remote nr database on NCBI's servers.
Is there a quick and easy way to get it to do these iterations for me without having to manually parse the results of PSI-BLAST and then using the results in a new PSI-BLAST call?