QUERY: Search programs for secondary structure

[Ashok Aiyar]

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:
ftp://ftp.mcs.anl.gov/pub/futures-lab/CAVE/scan_for_matches.tar.gz

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

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