Hi Troy,
MODELLER uses a Dynamic Programming algorithm (implemented in ALIGN method) to search for possible templates for a given target. It aligns the target with a list of given templates using ALIGN command. One can adjust gap penalties, overhangs, off_diagonal, etc... (see ALIGN commad) to search. Once all scores for the alignments between the target and the templates are calculated, SEQUENCE_SEARCH command calculates a significant score and sorts the output by this significant score. Sequences related to the target usually have Z-scores larger than 4 or 5 (see log file column SIGNIF).
For more information you can go to ALIGN command page: http://salilab.org/modeller/manual/node79.html or SEQUENCE_SEARCH command page: http://salilab.org/modeller/manual/node88.html in MODELLER 4 manual.
Best, Marc
Troy Wymore wrote: > > Hello MODELLERs, > > Could someone inform me on how MODELLER performs the search for templates > given a sequence? I could not tell from the manual what algorithm it was > using to do this. > > Thanks, > > Troy Wymore