RNA secondary structure database search

Eddy Sean sre at al.cam.ac.uk
Tue Jun 21 09:22:07 EST 1994

In article <940620213039.267 at jason.uthct.edu> ZWIEB at JASON.UTHCT.EDU (Christian Zwieb) writes:
  >Please, respond directly to Niels. He asks:

I'm forwarding this to Niels via email as well.

  >Is there to anyone's knowledge a program and/or a server, which allows
  >the user to input an arbitrary primary and secondary structure motif
  >to the Genbank/EMBL databases and have matches returned so they are
  >readable to both humans and computers? 

Besides Rodger Staden's motif searcher, I know of at least two
programs that have been written for RNA secondary structure pattern
searching.  One is RNAMOT, by Daniel Gautheret (CABIOS 6:325-331
1990). I think Gautheret is now in Boulder, at
gauthere at beagle.colorado.edu. I bet the program is still available
from him. A second option is my program RNABOB, which is a shameless
ripoff of RNAMOT look and feel but with a generally faster underlying
algorithm. It'll read GenBank and EMBL flat files.  RNABOB is freely
available via anonymous ftp from cele.mrc-lmb.cam.ac.uk in pub/sre, in
a distribution fit for most UNIX systems.

Both programs need a user-supplied pattern that describes a
non-stochastic primary sequence and secondary structure consensus.
I.e., the pattern is regular-expression-like, not profile-like. If you
need super-sensitive searching with a stochastic (probabilistic) RNA
sequence/structure pattern, there's software for that too (see
README-COVARIANCE-MODELS in pub/sre of the anonymous ftp server
cele.mrc-lmb.cam.ac.uk), but these algorithms are still too
computationally intensive for a search across all of GenBank/EMBL.

- Sean Eddy
- MRC Laboratory of Molecular Biology, Cambridge, England
- sre at mrc-lmb.cam.ac.uk

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