* psi-tblastn implementation (see tblastn_app.cpp)
* in_msa option to PSI-BLAST

* Alignment results: Dense-seg vs. disc (fails for remote blast)
* Remote searches: obtaining BLAST database information for formatter
* BlastOptions: setting of extra parameters

* Support PSSM checkpointing in psiblast (+tests)
* Make sure that proper error checking is done when recovering from saved
  search strategies, ie.: blastn search strategy provided to blastp

* remote PSI-BLAST
blast4 issues
* LongestIntronLength for translated searches
* DustFilteringparams for blastn
* SegFilteringWindow



Deferred items
* Should C toolkit checkpoint files be accepted? Provide conversion tool?
* Should we port patseed[pn]?