Structural RNA, folding energy and asymptotic Z-scores
Speaker: Peter Clote , BC/ Dept of Biology, Dept of Computer Science (courtesy)
Date: February 28 2005
Time: 11:30AM to 1:00PM
Location: 32-G575
Host: Bonnie Berger, MIT- Dept of Mathematics, CSAIL & HST
Contact: Kathleen Dickey, 617 253-3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/
We present results of computer experiments, which indicate that certain RNAs for which
the native state (minimum free energy secondary structure) is functionally important
(tRNAs, type III hammerhead ribozymes, selenocysteine insertion
sequences, signal recognition particle RNAs, small nucleolar spliceosomal RNAs,
riboswitches, 5S rRNA) all have lower folding energy than random RNAs of the same
length and dinucleotide frequency.
Additionally we find that whole mRNA as well as 5' UTR, $3'$ UTR, and cds regions of
mRNA have folding energies comparable to that of random RNA, although there may be
a statistically insignificant trace signal in $3'$ UTR and cds regions.
Various authors have used nucleotide (approximate) pattern matching and the
computation of minimum free energy as filters to detect potential RNAs in ESTs and
genomes. We introduce a new concept of asymptotic Z-score and describe a fast,
whole-genome, scanning algorithm to compute asymptotic minimum free energy Zscores
of moving window contents. Asymptotic Z-score computations offer another filter,
to be used along with nucleotide pattern matching and minimum free energy
computations, to detect potential functional RNAs in ESTs and genomic regions.
This is joint work with F. Ferre, E. Kranakis and D. Krizanc.
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