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Re: SEQUENCE_SEARCH



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

-- 
Dr. Marc A. Marti-Renom      |  phone : (212) 327 7206
The Rockefeller University   |  fax   : (212) 327 7540
1230 York Avenue, Box 38     |  e-mail: 
New York, NY 10021-6399      |  http://salilab.org/~marcius