QUERY: Search programs for secondary structure

Chris Patil cpatil at itsa.ucsf.edu
Sat Mar 15 14:20:19 EST 1997

I am looking for a program that can search databases for secondary
structure motifs, e.g., if I know that I have a stem-loop structure with
certain conserved residues in the stem and loop but otherwise satisfying
the secondary structure requirements alone, how can I look for such things
in a sequence database?

I know there are programs designed to look for tRNAs; I suppose something
similar would be useful here.

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