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Request: RNA folding prog. w/ ~2.5 kb RNA?

David Konerding rafael at cse.ucsc.edu
Thu Jun 30 10:08:55 EST 1994

Sean Eddy (sre at al.cam.ac.uk) wrote:
: In article <2ut37o$h9a at tierra.santafe.ede> stadler at SantaFe.edu (Peter Stadler) writes:
:   >We have been successfully folding 23S RNAs on an IBM RISC 6000/550
:   >with 64MByte memory and the complete genome of the phage Qbeta on
:   >an maschine with 256MByte. 

: You can look at suboptimal foldings from Michael Zuker's algorithm and
: say you succeeded because the presumed correct structure is within x%
: of the global minimum, but you can only say that because you know the
: correct structure (say, from comparative sequence analysis).  If
: you're dealing with a new structure, how do you pick the correct guy
: out of the haystack of suboptimals?

	Important question.  As an amusing aside, this year has been quite
an interesting one for me, as I have started to work on some programs for
the Computational Biology group at UC Santa Cruz.  The group is mainly
composed of computer scientists with knowledge quite specific to the realm of
solving computer problems, not biology problems.

	For a good part of the year, the difficulty I've had is in communicating
to the CS people that the "optimal" solution is not always what you want :-)

: The level of faith in RNA secondary structure prediction is sometimes
: shocking:

: "The credibility of the resulting structures did not seem to be an
: issue. There is even an unsubstantiated rumor (worth repeating) that
: when Brosius, Noller, and their colleagues submitted the first 16S
: rRNA sequence for publication, one of the reviewers questioned why
: they had not included the molecule's secondary structure as well!"
:              - Woese and Pace, in _The RNA World_, CSH Press, 1993

	Heh!  Noller was my Biochem 100A professor at UC, and is now sponsering
my thesis.  I think he may have submitted a secondary structure for publication
now-- using an interesting method of phylogenetic comparison of 16S --
"red dot green dot", and now the Comp Bio group at Santa Cruz has adopted this as
a new method of generating 16S structure.

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

  O~_    ---------------  David Konerding (University of California, Santa Cruz)
 c/ /'   ---------        rafael at cse.ucsc.edu
( ) \( ) -----            rafael at cats.ucsc.edu

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