TBI-Preprint 06-01-001
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Titel:
Partition Function and Base Pairing Probabilities of RNA Heterodimers
Author(s):
Stephan Bernhart,
Hakim Tafer,
Ulrike Mückstein,
Christoph Flamm,
Peter F. Stadler,
Ivo L. Hofacker
Submitted to:
Alg. Mol. Biol. 2006
Abstract:
Background:
RNA has been recognized as a key player in cellular regulation in recent
years. In many cases, non-coding RNAs exert their function by binding to
other nucleic acids, as in the case of microRNAs and sno{RNA}s. The
specificity of these interactions derives from the stability of
inter-molecular base pairing. The accurate computational treatment of
RNA-RNA binding therefore lies at the heart of target prediction
algorithms.
Methods: The standard dynamic programming algorithms for computing
secondary structures of linear single-stranded RNA molecules are extended
to the co-folding of two interacting RNAs.
Results:
We present a program, RNAcofold, that computes the hybridization
energy and base pairing pattern of a pair of interacting RNA molecules. In
contrast to earlier approaches, complex internal structures in both RNAs
are fully taken into account. RNAcofold supports the calculation
of the minimum energy structure and of a complete set of suboptimal
structures in an energy band above the ground state. Furthermore, it
provides an extension of McCaskill's partition function algorithm to
compute base pairing probabilities, realistic interaction energies, and
equilibrium concentrations of duplex structures.
Availability:
RNAcofold is distributed as part of the Vienna RNA
Package from
http://www.tbi.univie.ac.at/RNA/
Keywords: RNA secondary structure, folding algorithms, base pairing probabilities, hybridization
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Last modified: 2006-05-10 10:18:09 xtof