QUERY: Search programs for secondary structure

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Sat Mar 15 17:56:31 EST 1997

On 15 Mar 1997 19:20:19 GMT, Chris Patil <cpatil at itsa.ucsf.edu> wrote:
>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?

Take a look at Ross Overbeek's "Scan for Matches".  ANSI C source code
is available from the URL:

I have used scan_for_matches to search for symmetric palindromes (with
or without mismatches), and hairpins in both DNA and RNA sequences.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

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