Organization: Sali's Lab at The Rockefeller University
Reply-to:
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