... WU-Blast, psi-Blast, SIM, BLAT, MUMmer, Quasar, etc. ... Suffix tree: MUMmer, Quasar, REPuter. Only good for precise matches, highly similar sequences. ...
Linear Program Approach to Protein Threading. Relevance of Protein Structure ... Jackal (http://honiglab.cpmc.columbia.edu/programs/jackal/intro.html) CASP/CAFASP ...