On Thu, Jun 24, 2004 at 02:36:41PM -0400, noha lim wrote: > I just started using modeller a few weeks ago. > And now I'm doing an example(seq_search.top) in the website. > But it takes so long time(about 3 hours). > And I think that's right, because in the seq_search.log file from website > it also took 2 hours. > Then why is it so slow? > Others(like BLAST or something) take only a few seconds to find sequences. > What are the big differences??
Modeller's SEQUENCE_SEARCH command uses rigorous Smith-Waterman alignments in the search. These are guaranteed to be exact, but are expense to evaluate because of the large matrix used in the dynamic programming algorithm. BLAST, FASTA and similar programs use a word based heuristic to make alignments; this is a lot faster but gives only approximate alignments. Try a Google search for "Blast heuristic" to get more information.
Ben Webb, Modeller Caretaker